Manual Equipo Clarus400-480

GAS CHROMATOGRAPHY
CLARUS 400/480 GC
Software Guide
Clarus 400/480 GC
Software Guide
Release History
Part Number
Release
09936812
Publication Date
February 2010
Any comments about the documentation for this product should be addressed to:
User Assistance
PerkinElmer, Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.
Or emailed to: info@perkinelmer.com

Notices
The information contained in this document is subject to change without notice.
Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no
warranty of any kind with regard to this document, including, but not limited to, the implied
warranties of merchantability and fitness for a particular purpose.
PerkinElmer shall not be liable for errors contained herein for incidental consequential damages in
connection with furnishing, performance or use of this material.
Copyright Information
This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form whatsoever or
translated into any language without the prior, written permission of PerkinElmer, Inc.
Copyright 2010 PerkinElmer, Inc.
Produced in the USA.
Trademarks
Registered names, trademarks, etc., used in this document, even when not specifically marked as such,
are protected by law.
PerkinElmer is a registered trademark of PerkinElmer, Inc.
Clarus 400 GC is a trademark of PerkinElmer, Inc.
Clarus 480 GC is a trademark of PerkinElmer, Inc.
Table of Contents
Introduction ................................................................................................... 9
About This Manual ....................................................................................... 11
Manual Conventions and Screen Abbreviations ........................................... 13
Manual Conventions .............................................................................. 13
Screen Abbreviations ............................................................................. 13
Glossary of Clarus GC Terms ....................................................................... 15
Autosampler Terms ............................................................................... 15
Instrument-Specific Terms .................................................................... 16
Glossary of Chromatographic Terms ............................................................ 17
Symbols Located on the Clarus 400/480 GC ................................................ 20
System Description...................................................................................... 21
Introduction ................................................................................................... 23
Overview of the Clarus 400/480 GC............................................................. 24
About the Keyboard ...................................................................................... 26
About the Screen ........................................................................................... 27
Function Key Descriptions ........................................................................... 28
Method Function Key ............................................................................ 29
System Function Key ............................................................................. 29
Auto(sampler) Function Key ................................................................. 30
Background Function Key ..................................................................... 30
Control Key Descriptions ............................................................................. 31
Run Key ................................................................................................. 31
Reset Oven Key ..................................................................................... 31
Status Escape Key.................................................................................. 32
Delete Key ............................................................................................. 32
Entry Keys .................................................................................................... 33
Parameter Keys ............................................................................................. 34
Status, Menus and Screens ......................................................................... 35
Overview ....................................................................................................... 37
Turning on the System .................................................................................. 38
System Status ................................................................................................ 39
Checking the Status of Individual Items ....................................................... 41
Checking the Oven Temperature ........................................................... 41
Checking the Injector Temperature ....................................................... 41
Checking the Detector Temperature ...................................................... 42
Checking the Carrier Gas Pressure or Flow........................................... 42
Action Menus ................................................................................................ 44
Scrolling Through Menu Pages ............................................................. 44
Selecting an Option................................................................................ 44
3
Escaping from a Menu ........................................................................... 45

Input Screens................................................................................................. 46
Changing a Value on an Input Screen ................................................... 46
Initial Setup Procedures ............................................................................. 47
Configuration Basics ..................................................................................... 50
Displaying Configuration Screens ......................................................... 50
Configuring the Carrier Gas Pressure Units ................................................. 52
Configure the Carrier Gas Pressure Display .......................................... 52
Configuring Your Clarus 400/480 GC .......................................................... 53
Configuring the Autosampler........................................................................ 54
Configuring the Oven ................................................................................... 56
Configuring a Sleep Time ............................................................................. 57
How Sleep Works .................................................................................. 57
Setting an Oven Heating Delay ..................................................................... 59
Setting the Real Time Clock and Startup Time ............................................ 60
Configuring an Injector ................................................................................. 62
Configuring Carrier Gas Operation............................................................... 63
Configuring the Carrier Gas Operation ................................................. 63
Configuring Valves ....................................................................................... 65
Configuring Detectors ................................................................................... 66
Configuring a Recorder and/or Integrator ..................................................... 69
Configuring Integrator/Recorder Offsets ...................................................... 70
Configuring a Printer .................................................................................... 71
Setting Up Detectors ................................................................................... 73
About this Chapter ................................................................................. 75
Setting up a FID ..................................................................................... 76
FID Overview ............................................................................................... 77
Setting Up a Manual Pneumatics FID........................................................... 78
FID Setup Summary .............................................................................. 78
1. Connect a Flowmeter to the FID Collector .................................... 78
2. Adjust the Hydrogen Flow ............................................................. 80
3. Adjust the Air Flow ........................................................................ 83
4. Ignite the Flame .............................................................................. 84
Using the FID in Corrosive Environments ................................................... 88
Setting up an ECD ........................................................................................ 89
United States Government Regulations for ECDs ................................. 90
Special Instructions for ECD Cell Purchasers ....................................... 90
Labels..................................................................................................... 90
Leak Testing .......................................................................................... 91
Cell Failure or Damage .......................................................................... 91
Reporting Radiation Incidents, Theft or Loss ........................................ 91
Other Requirements ............................................................................... 91

United Kingdom Regulations ....................................................................... 92
ECD Overview .............................................................................................. 93
Setting Up an ECD........................................................................................ 96
ECD Setup Summary ............................................................................. 96
1. Vent the ECD Outlet ...................................................................... 96
2. Adjust the Make-up Gas Flow ........................................................ 99
Setting Up a TCD........................................................................................ 101
TCD Overview..................................................................................... 101
Setting Up a TCD........................................................................................ 102
TCD Setup Summary ........................................................................... 102
1. Turn on the Oven and Detector Heaters ....................................... 102
2. Equalize the Makeup and Reference Gas Flows .......................... 103
3. Enter the TCD Bridge Current Range .......................................... 105
4 Balance the Bridge ....................................................................... 106
Using a TCD with the Autosampler or GSV .............................................. 107
Setting Up a NPD........................................................................................ 108
NPD Overview ............................................................................................ 109
Setting Up a Manual Pneumatics NPD ....................................................... 111
NPD Setup Summary ........................................................................... 112
1. Disconnect the Hydrogen and Air Lines at the NPD Bulkhead ... 112
2. Adjust the Hydrogen Flow ........................................................... 113
3. Adjust the Air Flow ...................................................................... 114
4 Reconnect the Air and Hydrogen Lines ....................................... 115
NPD Bead Activation Procedure ......................................................... 116
Controlling the Clarus 400/480 GC ......................................................... 123
Overview ..................................................................................................... 125
Viewing Active Method Parameters ........................................................... 126
Active Method Parameter Examples ................................................... 128
Editing the Active Method .......................................................................... 129
Getting Ready to Edit the Active Method ........................................... 129
Setting Up Oven and Inlet Temperature Programs .............................. 130
Setting Injector Temperatures.............................................................. 136
Viewing or Adjusting Carrier Gas Pressure......................................... 138
Setting the Septum Purge Mode and Offset......................................... 139
Setting Up Valves ................................................................................ 140
Setting Detector Temperatures ............................................................ 140
Setting the Range ................................................................................. 142
Changing TCD Polarity During a Run ................................................ 145
Routing Detector Output ............................................................................. 146
Rerouting Output ................................................................................. 146
Building a Timed Events Table ........................................................... 151

Method Utilities .......................................................................................... 159
Generating a Method ........................................................................... 159
Setting Up a Stored Method................................................................. 161
Copying a Method ............................................................................... 162
Deleting a Stored Method .................................................................... 162
Editing a Stored Method ...................................................................... 163
Printing a Method ................................................................................ 164
Controlling the Autosampler ................................................................... 165
Overview ..................................................................................................... 167
Autosampler Trays and Carousel ......................................................... 168
Syringe Wash Parameters ........................................................................... 171
Injection Mode Parameters ......................................................................... 172
Running Samples in Single-Program Mode................................................ 174
1. Configure for Single-Program Mode............................................ 174
2.
Enter Single-Program Mode Parameters .................................. 175
3. Set Up a Method ........................................................................... 177
4. Start the Autosampler ................................................................... 177
Running Samples in Multi-Program Mode ................................................. 178
1. Configure for Multi-Program Mode ............................................. 178
2. Enter Program 1 Parameters ......................................................... 179
3. Enter Program 2 Parameters ......................................................... 181
4. Start the Autosampler ................................................................... 181
Other Autosampler Tasks ........................................................................... 183
Using Solvent Pre-Washes................................................................... 183
Running Viscous Samples ................................................................... 184
Cleaning the Syringe............................................................................ 185
Printing ................................................................................................ 186
Pausing and Resuming an Autosampler Program ................................ 187
Stopping the Autosampler ................................................................... 188
Parking the Autosampler Tower .......................................................... 188
Inserting a Priority Sample .................................................................. 188
About Waste and Wash Vials ..................................................................... 190
Single-Program Mode .......................................................................... 190
Multi-Program Mode ........................................................................... 190
About Sample Vials .................................................................................... 191
Using a TCD with the Autosampler ............................................................ 192
Available Syringes ...................................................................................... 192
Background Compensation ...................................................................... 193
Overview ..................................................................................................... 195
Calibrating a Baseline Profile ..................................................................... 196
Calibration Menu Options ................................................................... 196

Turning Background Compensation On .............................................. 198
Turning Background Compensation Off ............................................. 198
System Utilities .......................................................................................... 199
Overview ..................................................................................................... 201
Using the Built-in Stopwatch ...................................................................... 202
Configuring the Clarus GC ......................................................................... 204
Entering the Configuration Mode ........................................................ 204
Displaying Configuration Menus......................................................... 204
Calibrating the Flow Readout Using Manual Pneumatics .......................... 206
Printing the Run Log ................................................................................... 210
Printing the System Configuration .............................................................. 211
Locking and Unlocking the Keyboard ........................................................ 212
Calibrating the Oven Temperature .............................................................. 213
1. Calibrate the Reference Thermometer.......................................... 213
2. Place the Thermometer Probe in the Oven ................................... 213
3. Equilibrate the Oven Temperature ............................................... 215
4. Enter the Required Offset Value .................................................. 216
5. Remove the Thermometer Probe .................................................. 216
Deconfiguring and Configuring Injectors ................................................... 217
Deconfiguring and Configuring Detectors .................................................. 219
Appendix: Configuration Menus ............................................................. 221
Displaying Configuration Menus ................................................................ 224
Configuration Menu Examples ................................................................... 225
Going Directly to a Primary Configuration Menu ...................................... 227
Index ........................................................................................................... 229
Introduction
Clarus 400/480 GC Software Guide
About This Manual

The Clarus 400/480 GC Hardware and Software Manual is your complete detailed guide to
setting up the Clarus 400 GC or Clarus 480 GC and integrated autosampler in preparation for
running samples.
This manual contains information and procedures for all of the available injectors and
detectors. To benefit the most from this manual, we recommend that you read all of the
chapters in sequence and follow the procedures provided that apply to your specific injectors
and detectors as closely as possible. In most cases, reading one chapter is a prerequisite for
going on to the next.
For detailed safety information please refer to the Clarus 400/480 GC Installation Guide
(09936810).
11
Introduction
The manual consists following chapters:

Chapter 1
Introducing the Clarus 400/480 GC describes the Clarus GC

and its major features, including keyboard and display
descriptions.
Chapter 2
System Description describes the Clarus GC and its major

features, including keyboard and display descriptions.
Chapter 3
Status, Menus, and Screens introduces you to the look and feel
of Clarus GC user interface. It shows you how to turn on the
GC, check the status, and perform fundamental operations such
as changing parameters, selecting options, etc.
Chapter 4
Initial Setup Procedures contains configuration procedures that

you should perform before using the Clarus GC for the first time.
Chapter 5
Setting Up Detectors contains subsections that describe how to

set up each of the following detectors: FID, ECD, TCD and
NPD.
Chapter 6
Controlling the Clarus 400/480 GC describes how to set

operating parameters including procedures for controlling
heaters, setting up, editing, copying, deleting, generating, and
printing methods.
Chapter 7
Controlling the Autosampler describes autosampler screen

menus and parameters. Procedures are included for setting up
autosampler programs.
Chapter 8
Background Compensation describes how to set the background

compensation for your detector signals.
Chapter 9
System Utilities contains procedures for using the built-in

stopwatch; calibrating the optional flow readout; printing
configuration parameters or run logs; locking and unlocking the
keyboard; calibrating the oven; and deconfiguring and
configuring injectors and detectors.
Appendix
Examples of Configuration Menus.
Index
12
Manual Conventions and Screen Abbreviations

Manual Conventions
Individual keys are displayed in the text by enclosing the name of the key in square brackets.
For example, [Oven Prog], [Enter], [->Set], [Method], [System], [1], [8], etc.
All temperatures are in degrees Celsius (C).
Screen displays are presented throughout the text as a double-lined box:
Method 1
READY
75
Screen Abbreviations
Autosamp autosampler
AUX Auxiliary zone
Cap capillary split/splitless injector
Cmptr computer
Ctrl syringe control parameters
ECD Electron Capture Detector
Equil equilibration
Extrn external
FID Flame Ionization Detector
Gen generate
GSV gas sampling valve
Inj injector
Inj/Vial injections per vial
Int integrator
kPa kilopascals
NPD Nitrogen Phosphorus Detector
OnCol on column
13
Introduction
Ovn oven
Paus pause
Pkd packed injector
Pre # of preinjection syringe washes
Pres pressure
Prg autosampler program
Pri priority sample vial
Psi or psig pounds per square inch (gauge)
Rec recorder
Resm resume
Stpwtch stopwatch
TCD Thermal Conductivity Detector
14
Glossary of Clarus GC Terms

The glossary of Clarus GC terms are divided into two types:
*
Autosampler Terms
Instrument-Specific Terms
Autosampler Terms
Term
Description
Washes
Washing the syringe.
Pre
The number of prewashes of sample to prime the syringe (no

pumping).
Post
The number of post injection syringe washes with a solvent.
Pumps
The number of times the syringe draws up sample and

evacuates it before acquiring the volume. This is done to
eliminate bubbles.
Mode
The style of injection.
Fast
Fast speed of the syringe during sample injection. This is used

to eliminate discrimination in the needle.
Normal
Normal speed of the syringe during sample injection.
Slow
Slow speed of the syringe during sample injection in order to

inject directly into a wide-bore capillary column, in hot
injection port.
Solv
The number of solvent washes performed before the

preinjection sample washes.
Visc
The number of seconds the plunger pauses when drawing up a

viscous sample into the syringe.
15
Introduction
Instrument-Specific Terms
Term
Description
Background
compensation
A routine that automatically subtracts a stored calibrated

baseline profile from the signal generated during a GC run.
Ballistically
Changing the oven temperature as quickly as possible to reach

a set point.
Detector
background
The detector output signal when no components are being

eluted.
Equilibration
The delay time after the method set points have been reached
before the system becomes READY.
Isothermal method
A method in which the oven temperature remains constant

throughout a GC run.
Method
A collection of parameters that control the GC.
Negative-time
event
A timed event that you set to occur before the instrument

becomes READY.
Parameter
An independent variable used to specify a condition to be met.
Pre-run
The time after equilibration during which negative-time events

are executed.
Range
For a Flame Ionization Detector, range means amplification of

the detector output signal. For a Thermal Conductivity
Detector, range means the bridge current.
Ready
Indicates that all method parameters have reached their set

points and that you can start your analysis.
Run
The time from sample injection to the end of the oven

temperature program.
Sleep mode
The GC can be set to a predefined method for gas savings.
Timed Events
Events that take place before or during a GC run as

specified in a timed events table.
Zone
A heated area in the GC oven, injector, or detector.
16
Glossary of Chromatographic Terms*

Adsorption A process that occurs at the surface of a liquid or solid as a result of the
attractive forces between the adsorbent and the solute. These forces may be physical or
weakly chemical.
Analysis The complete investigation of a sample by gas chromatographic separation
including identification of the sample components and quantitative measurements.
Anode The negatively charged electrode in any electrical circuit to which charged particles
and ions are attracted.
Band Broadening A process that occurs in the GC whereby the peak width for a
component increases the longer the component travels through the column.
Baseline The detector signal to a recorder or integrator when only the carrier gas is passing
through the detector.
Baseline drift Any regular change occurring in the baseline signal from the detector,
usually resulting from column temperature and/or gas flow changes.
Blank run A run without the sample being injected.
Bleed The evaporation of the stationary phase from a column.
Capillary column (wall coated open tubular column) A small-internal-diameter column
whose inside wall is coated with a liquid phase.
Carrier gas The mobile phase of the separation system. An inert gas which transports the
sample from the injector through the column to the detector. This gas is usually helium,
hydrogen, or nitrogen.
Column conditioning A process for producing a stable column by heating the column with
carrier gas flowing to remove volatile impurities from the stationary phase.
Detectors Hardware that responds to sample components producing an electrical signal that
can be measured to quantitate the amount of each component present.
Flow rate The mass flow of carrier gas or detector gas in milliliters per minute.
Ghost peaks Peaks that are not due to sample components, for example, peaks produced by
carrier gas impurities, septum, or components from previous analyses.
Injection port The hardware through which the sample is introduced to the column by
injection.
*
Reference: Denney, R.C. A Dictionary of Chromatography.
17
Introduction
Linearity Quantitatively all detectors will produce a linear response with respect to solute
concentration over a defined range, for example, the Linear Range.
Liquid phase The material in the column that causes the components to separate because of
partitioning of the components between the mobile phase (carrier gas) and the stationary
phase (liquid phase).
Lowest limit of detection The smallest amount of sample that can be detected by the
detector being used. Usually defined as any signal that is as great as two times the noise
level. Also referred to as Minimal Detectable Quantity (MDQ).
Mobile phase The gas which carries the solute (sample) along and over the column
material. This carrier gas is inert and usually helium, nitrogen, or hydrogen.
Noise Background signal fluctuations arising from a detector response. This response is the
result of the column installed, carrier gas purity, electronic components, etc. The
response of any detector is defined by the signal-to-noise ratio.
Partition Coefficient The differential solubility of a substance in two different phases. In
the case of gasliquid chromatography, the sample components reach an equilibrium
between the gas phase (mobile) and the liquid phase (stationary). Each component has a
different partition coefficient thus causing separation in the column.
Resolution The degree of separation between two peaks.
Retention time The time interval from the point of injection to the appearance of the peak
maximum, of a components signal.
Septum Silicone rubber material placed in the injection port through which the injection is
made. When the needle is withdrawn, the silicone rubber reseals, thus not allowing any
sample or carrier gas to escape.
Stationary phase The liquid or solid adsorbent portion of the column that retains
components passing through the GC column.
Syringes Precision dispensing devices used to deliver sample to the GC. Liquid and gas
syringes are available.
Tailing When a peak is not symmetrical or Gaussian shaped but the back end is broadened,
it is said to be tailing.
Temperature programming A technique commonly used to increase the rate of elution of
the components. After the sample is injected into the oven at a specific temperature, the
temperature program increases the oven temperature to the prescribed temperature at a
defined rate (in C/min).
18
Unretained peak A component that is not retained by the column. The time taken for an
unretained sample to pass through the column is the same time as the time taken for the
carrier gas to pass through.
19
Introduction
Symbols Located on the Clarus 400/480 GC
PNEUMATIC SYMBOL
LEGEND
CARRIER
FLOW / PRESSURE
FID
TCD
NO CONNECTION
20
DETECTOR MAKE-UP/
REFERENCE FLOW
HYDROGEN
AIR
NPD
SPLIT FLOW
ECD
System Description
22
Introduction
The Clarus 400 and Clarus 480 Gas Chromatograph is a dual-channel, temperatureprogrammable stand-alone gas chromatograph (GC). It is available in many configurations, such
as with or without, an autosampler and a variety of injector/detector combinations to provide you
with total GC flexibility. The Clarus GC is microprocessor controlled, where you enter the
operating parameters from the color-coded keyboard and view the prompting text and monitor
instrument functions on a large two-line vacuum fluorescence display.
Figure 1. The Clarus GC.
23
System Description
Overview of the Clarus 400/480 GC

Your Clarus GC may have none, one, or two of the following detectors installed:
Flame Ionization (FID)
Electron Capture (ECD)
Nitrogen Phosphorus (NPD)

Thermal Conductivity (TCD)
The FID, ECD, TCD, or the NPD, may be installed in either the front or the rear detector
position.
Each installed detector has one analog output which may be attached to either an integrator or
recorder. Signals may be routed under instrument control.
Either none, one, or two packed column injectors; none, one, or two capillary column
injectors; or one of each injector type may be installed. Capillary column injectors consist of
the conventional split/splitless injector (CAP).
Up to two gas sampling valves may be installed.
The Clarus 400 and Clarus 480 GC is a manual pneumatics instrument.
The carrier gas and detector gas controls are built into the pneumatics control panel on the
Clarus GC. The carrier gas controls are used to set the flow for packed injectors and the
pressure for CAP injectors. The detector gas controls are used to set the hydrogen and air for
FID and NPD reference for TCD; and make-up gas for the ECD. Figure 2 is an example of a
dual-channel pneumatics control panel with Channel 1 containing a capillary injector and a
FID and Channel 2 containing a packed injector and an ECD.
For each channel, the injector-pneumatic controls are on the left and the detector-pneumatic
controls are on the right.
24
Channel 1
Channel 2
Figure 2. Example of a dual-channel pneumatics control panel in the Clarus GC.

Channel 1 designates an injector/detector combination installed in the front position of the
instrument, whereas Channel 2 designates a injector/detector combination installed in the rear
position.
25
System Description
About the Keyboard

The keyboard is your link to the software. The keyboard keys divided into the following
groups:
Note:
Function keys
Parameter keys
Entry keys
Control keys
As you run this instrument you will see software functions on the display that are
not supported by the Clarus GC. Please ignore these functions and continue with your
analysis.
An audible short beep sounds every time a key is pressed. A long beep sounds when an error
has been made. The key groups and their locations are illustrated in Figure 3.
Function Keys
Method
System
Auto
BackGround
Run
Parameter Keys
Entry Keys
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
0 no
Control Keys
Figure 3. The Clarus 400/480 GC keyboard.
26
About the Screen

The Clarus GC screen is a 2-line by 20-character vacuum fluorescent display.
Method 1
Ready
245 C
Figure 4. Vacuum fluorescent screen.
The screen displays status information, error messages, and interactive menus (method,
system, configuration, autosampler, and background).
27
System Description
Function Key Descriptions

The four function keys, [Method], [System], [Auto], and [Background], give access to the
top-level software menus. The [System] menu, in addition to presenting a number of system
utility options, provides access to the Configuration Mode.
Pressing a function key displays either a one-page menu or the first page of a two-page menu
associated with that key.
Method
System
Auto
BackGround
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
Figure 5. Function keys.
28
Run
0 no
Method Function Key
Pressing [Method] displays the first page of the two-page Method Menu.
Method 1
Setup Edit
Active
Copy
>
Method Menu, Page 1
Method 1
Gen Delete
Active
Print
>
Method Menu, Page 2
The commands in the Method Menu provide utilities for managing and editing methods.
Procedures for using these utilities are given in Controlling the Clarus 400/480 GC chapter.
The following table is a brief description of these utilities.
Command
Description
Setup
Sets up a Stored Method as the Active Method. This option is

not available during a GC run or with active automation.
Edit
Allows you to display and edit a Stored Method.
Copy
Copies an existing method to another method number.
Gen
Allows you to generate a new method from the default method.
Delete
Allows you to delete one of the Stored Methods.
System Function Key

Pressing [System] displays the Page 1 of the two-page System Control menu.
System Control
Config
Lock >
System Control Menu, Page 1
System Control
Stpwtch Extrn Prnt
>
System Control Menu, Page 2
The commands in the System Control menu provide a number of system utilities.
Procedures for using these utilities are given in chapter 9, System Utilities. A brief
description of these utilities follows.
29
System Description
Command
Description
Config
Selecting this option puts the system into the Configuration Mode.
The configuration menus allow you to specify configuration details
for a variety of hardware options.
Lock
Locks or unlocks the keyboard. For procedural details see Locking

and Unlocking the Keyboard in Chapter 13, System Utilities.
Stpwtch
Accesses the stopwatch function. For procedural details see Chapter

13, System Utilities.
Extrn
Used to set up an external computer or printer.
Auto(sampler) Function Key

Pressing [Auto] displays the first page of the two-page Autosampler (A/S) menu.
A/S Stopped
Prg Ctrl START
Autosampler Menu, Page 1
>
A/S Stopped
Park Clean
Print >
Autosampler Menu, Page 2
The top line displays the autosamplers status (for example, Stopped). The bottom line
displays menu options.
Autosampler details are too specialized and extensive to be described in this chapter. All
details are provided in Chapter 7, Controlling the Autosampler.
Background Function Key
Pressing [Background] displays the Background menu on the bottom line and the
background status on the top line.
Background 1
Off
Calibrate
Detailed procedures for using this function are given in chapter 8, Background
Compensation.
30
Control Key Descriptions
Method
System
Auto
BackGround
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
Run
0 no
Figure 6. Control keys.
Run Key
Press the [Run] key to start a GC run after manually injecting a sample, continue to run after
an oven hold, or to initiate calibrating a background. Details for using [RUN] for the latter
purpose are given in chapter 8, Background Compensation.
Reset Oven Key
This key is used to reset the oven temperature during a run.

Reset to oven Temp
1
2
3
During the execution of a temperature program, you can elect to heat the oven ballistically to
a higher step by selecting the appropriate number from the menu.
31
System Description
Select 1 to stop a run and reset the instrument to the initial method conditions. Additional
details are given in chapter 6, Controlling the Clarus 400/480 GC.
Status Escape Key
The [Status Escape] key is used to escape from various environments. The top level to
which you can escape is the System Status screen.
Method 1
READY
75
A screen similar to that above appears if you escape from the Method, System, Autosampler,
or Background menus.
If you press [Status Escape] a second time, the screen displays the Run End Time, as shown
below.
Method 1
END
READY
13.0m
In the case of a submenu, escape brings you up to a previous menu level.
Delete Key
Use this key to delete a timed event or oven temperature program step.
32
Entry Keys
Method
System
Auto
BackGround
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
Run
0 no
Figure 7. Entry keys.

All Entry keys, except for the ->Set] key, are similar to those on a hand calculator and are
used to enter numeric data, clear an entry, etc.
The [CE] key (Clear Entry) is used to clear a value before it is entered or to clear certain error
messages from the screen.
The [On/Yes 1] and [Off/No 0] keys are multipurpose keys. In addition to using these keys
for entering a numeric 1 or 0, they are used to enter "On" or "Off, "Yes" or "No" in response
to questions requiring these answers.
The [->Set] key is used to move the screen cursor to a desired screen parameter or menu
option for selection. How to use this key for this purpose is described in the next chapter.
The [->Set] key is also used to activate the Autozero, and actuate connected valves.
33
System Description
Parameter Keys
Method
System
Auto
BackGround
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
Run
0 no
Figure 8. Parameter keys.

The Parameter keys are used to display operation or configuration parameters. Pressing a
Parameter key when you not in the Configuration Mode displays the operating parameter
associated with that key. Operating parameters are described in chapter 6, Controlling the
Clarus 400/480 GC chapter. In the Configuration Mode, pressing a Parameter key displays
the configuration of the hardware associated with that key.
34
Status, Menus and

Screens
36
Overview
This chapter introduces the Clarus 400/480 GC software and includes examples of how to:
Turn on the Clarus GC and interpret the system status screen.
Check the status of individual items such as the oven temperature, injector
temperature, etc.
Perform operations such as scrolling through menu pages, selecting an option,

entering/changing data.
A basic knowledge of the procedures in this chapter is required before you can perform the
tasks in the remaining chapters. We therefore recommend that you duplicate the examples
shown as closely as possible.
The examples shown in this chapter were prepared with a Clarus 400 GC containing the
following detectors and injectors:
Note:
A FID in detector position 1 (front)
An ECD in detector position 2 (rear)
A capillary injector in injector position 1 (front)
A packed injector in injector position 2 (rear)
not supported by the Clarus 400/480 GC. Please ignore these functions and continue with
your analysis.
CAUTION
If the display shows Sleep Mode do not activate this mode

since this function is only available in the PPC option. The
PPC option is not available on the Clarus 400/480 GC. If
you inadvertently select this option, reboot the Clarus
400/480 GC. Once the instrument is rebooted select the
Config screen and switch off the Sleep Mode so the Clarus
400/480 GC will function properly
37
Status, Menus and Screens
Turning on the System
On/Off Switch
Figure 9. Clarus 400/480 GC.

The On/Off switch is located on the lower right hand side of the Clarus GC (see above).
Upon completion of the power-on diagnostics, a System Status screen similar to that shown
below appears:
Method 1
Ovn Det Inj
NOT RDY
40
If an error message appears instead of the above screen, refer to the Clarus 400 /480 GC
Hardware Guide, Troubleshooting chapter.
38
System Status
Upon initial startup, the Clarus GC monitors the carrier gas inlet pressure. If this pressure is less
than 50 psi, the following message occurs.
Warning: Car1 Inlet
< 50 psi, Press CE
After you press CE, this message will not occur again, even if you did not correct the
situation.
Also at this time, the oven, injector(s), and detector(s) start heating to the set points specified
in the Active Method. Until all components reach their set points, the system is not ready for
an injection to be made. This is indicated by the message NOT RDY on the upper right
corner of the screen.
The system indicates the components that are not ready by displaying and blinking their
abbreviated names on the bottom line of the System Status screen. The bottom line also
shows the actual oven temperature and continuously updates it.
There is room on the screen for only three abbreviated names. As a component reaches its set
point, its abbreviated name disappears from the screen and is replaced by the next name in the
priority list that is not ready. The priority display order is as follows:
Ovn (oven temperature)
Det (detector temperature) If two detectors are installed, the appearance of "Det"
indicates that either or both detectors are not ready.
Inj (injector temperature) If two injectors are installed, the appearance of "Inj"
indicates that either or both injectors are not ready.
Gas (carrier gas flow/pressure) For the Clarus 400/480 GC, if a capillary injector
and a packed injector with the Optional Flow readout are both installed, the
appearance of "Gas" indicates that the carrier gas pressure/flow for one or both
injectors has not been adjusted to the set point.
39
Ext appears if the device attached to the READY IN terminal (for example, a data
handling system) is not ready. Please refer to the Clarus 400/480 Installation
Instructions for details.
When all components are READY, the system starts equilibrating and the NOT RDY
message changes to EQUILIB.
Method 1
-1.5 min
EQUILIB
75
The clock counts down until the equilibration time has elapsed. The Clarus GC is now
ready for a sample injection shown by displaying READY in the upper right corner of
the screen.
Method 1
40
READY
75
Checking the Status of Individual Items

You can check the set points and actual values for the following items at any time by pressing
the appropriate method parameter key:
Oven temperature [Oven Prog] key
Injector temperature [Inject Prog] key
Detector temperature [Detect Control] key
Carrier gas pressure and/or flow [Carrier Prog] key
On each menu, the set point is displayed on the bottom line and the actual value (which is
continuously updated) is displayed on the top line.
If the items set point and actual value are not equal (within a specified tolerance), then that
item is NOT READY and its abbreviated name appears on the System Status screen.
Checking the Oven Temperature
Press [Oven Prog]. A menu similar to the following appears:

Oven NOT RDY 40
Temp 1
75
The above example shows that the temperature of the oven has not reached the set point
of 75 C.
Checking the Injector Temperature
Press [Inject Prog]. A menu for the injector installed in position 1 (front) appears.
Cap 1 NOT RDY 110
Temperature
150
The above example shows that the temperature of the capillary injector installed in
position 1 has not reached the set point.
41
If a second injector is installed, you can check its temperature status by pressing
[Inject Prog] again.
Pkd 2 NOT RDY 160
Temperature
200
The above example is for a packed injector installed in position 2 (rear).
Checking the Detector Temperature
Press [Detect Control]. A menu for the detector installed in position 1 (front) appears.
FID 1 NOT RDY 120
Temperature
165
The above example shows that the temperature of the FID detector installed in position 1
has not reached the set point.
If a second detector is installed you can check its temperature status by pressing
[Detect Control] again.
ECD 2 NOT RDY 160
Temperature
200
The above example is for an ECD installed in position 2.
Checking the Carrier Gas Pressure or Flow

To check the carrier gas or pressure flow press [Carrier Prog].
A capillary injector is installed in position 1. A screen appears that shows the actual pressure
(top line) and the set point (bottom line). Examples of a NOT RDY and a READY screen
are shown below:
Pres 1 NOT RDY
10.2
Set
25.4 psi
Pres 1
Set
25.4
25.4 psi
1. Press [Carrier Prog] again to display the carrier gas screen for the injector installed in
position 2. The screen below shows that a packed injector with the optional Flow
Readout is installed in position 2.
42
Flow 2 NOT RDY

Set
25
30mL
2. To return to the System Status screen, press [Status Escape].

Note:
The procedure for setting carrier gas pressure is given in Clarus 400/480 GC Hardware
Guide Chapter 5, Installing a Capillary Column on a Capillary Injector. The procedure
for setting carrier gas flow is presented in Chapters 4 and 5 in the Clarus 400/480 GC
Hardware Guide.
43
Action Menus
An action menu is a display that contains options. When you select an option and press
[Enter], the microprocessor carries out the selected option.
To see an action menu, press [Method]. Page 1 of the Method menu appears.
Method 1
Active
Setup Edit
Copy >
This is the first page of a two-page menu. A menu contains a second page if the
character > appears on the far right of the bottom line.
Note:
When the Clarus GC is under external control (for example, Turbochrom) the method menu
is not available from the GC keyboard.
Scrolling Through Menu Pages
To see the second page, press [->Set] several times to scroll the
cursor ( ) off the right side of the display and onto the next page.
Method 1 Active
Gen Delete Print >
To go back to the first page, repeat the above procedure.

Alternatively, you can scroll from page to page by repeatedly pressing the function key
that produced the menu. In this case you would press the [Method] key.
Selecting an Option
When an action menu is displayed, the cursor ( ) appears on the bottom line to the left of the
default option. For example:
Method 1 Active
Setup Edit Copy >
1. To select a default option, simply press [Enter].
2. To select another option, press [->Set] until the cursor is on the left of the desired
option. To complete the selection, press [Enter].
44
If you select the wrong item, press [CE] before pressing [Enter] to restore the
cursor to its original position.
Escaping from a Menu
Press [Status Escape] to escape from a menu. This displays the next higher menu of the
System Status screen.
Method 1
Note:
READY
75
You may have to press [Status Escape] several times to display the status screen.
45
Input Screens
An input screen is one in which data are entered or modified. To see an example of an input
screen, press [Oven Prog]. A screen similar to the following appears:
Oven
TEMP 1
75
75
Changing a Value on an Input Screen

To change a value, in this case the oven temperature set point:
1. Type in the new value and notice that the cursor ( ) begins to blink. This indicates that
a new value is being typed.
2. Press [Enter] to accept the new value. The cursor stops blinking.
To restore the original value, press [CE] before pressing [Enter].
If your entry is not within the allowed range, an error message is displayed that
indicates the allowable range as shown in the following example:
Illegal Oven Temp
Range: xxx ---> yyy
Where xxx and yyy are the permissible minimum and maximum oven temperatures
respectively. If this message appears, press [CE] to restore the original value, type a
value within the allowable range, then press [Enter].
46
Initial Setup
Procedures
48
Your Clarus GC has been configured at the factory to correctly reflect the installed injectors
and detectors. However, there are operational parameters that you must configure before
using your Clarus GC. This chapter familiarizes you with the steps necessary to configure
your Clarus GC by using a typical configuration example.
Configuration Basics (on the next page), provides you with the background information
needed to perform the following tasks. More specifically, in this chapter you will learn how
to:
Enter the Configuration Mode.

Display configuration menus.
Configure the carrier gas display
Review or change the current configuration settings.
49
Initial Setup Procedures
Configuration Basics
Before configuring the Clarus GC, take time to familiarize yourself with the keyboard by
noting the location of the keys and how the keys are grouped. The following illustration
shows the key group locations on the Clarus 400/480 GC keyboard:
Function Keys
Method
System
Auto
BackGround
Run
Parameter Keys
Entry Keys
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
0 no
Control Keys
Figure 10. Clarus 400/480 GC Keyboard.

Note:
your analysis.
Displaying Configuration Screens
Before configuring your Clarus GC you can become familiar with all of the configuration
screens (menus) by first entering the Configuration Mode (by pressing [System] [Enter]) and
50
then repeatedly pressing [Enter] to view each screen. When viewing the last configuration
screen, pressing [Enter] returns you to the initial configuration screen. The total number of
configuration screens that appear depend on the particular hardware installed.
Once familiar with the overall configuration of your Clarus GC, you can go directly to most
configuration screens by doing the following.
To display a screen containing the
following information:
First enter the Configuration Mode by

pressing...
[System] [Enter]
... then press following key(s):
Oven Maximum Temp Limit Setting
[Oven Prog]
Oven Temp Calibration
[Oven Prog] [Enter]
Oven Equilibration Time
[Time]
Sleep Time
[Time] [Time]
Heating Delay Configuration
[Time] [Time] [Time]
Time of Day Clock
[Time] [Time] [Time] [Time]
Start Time
[Time] [Time] [Time] [Time] [Time]
Coolant Type
[Rate]
Injector Type
[Inject Prog]
Carrier Gas Display
[Carrier Prog]
Detector Settings
[Detect Control]
Output to a recorder/integrator
[Output]
Output Offset
[Auto Zero]
Autosampler Mode
[Auto]
51
Configuring the Carrier Gas Pressure Units

Before checking and configuring all of the Clarus GC parameters, we suggest that you first
configure the carrier gas pressure units.
Configure the Carrier Gas Pressure Display

Follow this procedure to configure the carrier gas display.
1. Press [System].
System Control
Confg
Lock >
2. Press [Enter] to select Confg, then press [Carrier Prog].

A screen similar to the following appears with unit choices for the gas display:
Gas Display 1
None kPa
Config
PSIG Flow
The gas display choices are:
Note:
None
If None is selected, there will be no carrier gas display for the

selected channel.
kPa
Selecting kPa displays the actual pressure in kilopascals.
PSIG
Selecting PSIG displays the actual pressure in pounds/square

inch.
Flow
Selecting Flow displays the actual flow in mL/min. Select flow

only if a carrier gas flow controller is installed in the selected
channel.
The gas display units are factory configured as PSIG.

To change the display to None, kPa, or Flow select the appropriate option, then press
[Enter]. This setting only affects the selected carrier gas channel.
3. Press [Status Escape] to return to the System Control menu.
52
Configuring Your Clarus 400/480 GC

Follow this procedure to view or change the configuration of your Clarus GC.
To enter the configuration mode:
1. If necessary, display the System Control screen by pressing [System].
The first page of the two page System Control menu appears as shown in the left screen.
System Control
Confg
Lock >
System Control
Stpwtch Extern >
If you want to display the second page, press [->Set] three times to display the screen on
the right.
Note:
Whenever you see " > " displayed on the screen, it indicates that there are additional menu
selections. Press the [->Set] key repeatedly to display those selections.
2. To enter the Configuration mode, if necessary, press [->Set] to move the cursor to the
left of Confg (as shown above), then press [Enter].
If the autosampler is installed, the
following screen appears:
If the autosampler is not installed,

the following screen appears:
Automation Configure
None AutoSamp
Oven Maximum Config

Temp Limit
450
53
Configuring the Autosampler

If your Clarus GC is equipped with an autosampler, follow this procedure to configure the
autosampler.
To configure the autosampler:
1. If necessary, first display the System Control screen by pressing [System].
The first page of the two page System Control menu appears:
System Control
Confg
Lock >
2. Press [Enter] to select Confg.

The following Automation Configure screen appears if an autosampler was detected
during power-up:
None AutoSamp
3. Press [->Set] to select AutoSamp, then press [Enter].
The Automation Configure screen appears:
Single Multi
Single
A single autosampler program that specifies which injector is to be used, the size
of the injection, and the number of injections per vial. Samples are injected
sequentially starting with the first occupied vial position. The GC is controlled
by the parameters in the Active Method.
Multi
The autosampler runs two programs consecutively. Each program specifies: the
method to be used (each program can use a different method if desired), which
injector to use, the size of the injection, the number of injections per vial, and the
starting and ending vial numbers. As each program is run, the system sets up the
specified method as the Active Method. While running in this mode, the
autosampler attempts at least one injection from each vial in the specified ranges.
4. Press [->Set] to select Single or Multi, then press [Enter].

54
The Automation Configure Recycle screen appears:

Recycle
Off
Turning On Recycle causes the autosampler's automation program to repeat after it has
finished.
5. Press [Enter].
The A/S Syringe Config screen appears:
A/S Syringe Config
0.5L 5.0L 50.0L
6. Press [->Set] to select the syringe size installed in the autosampler, then press [Enter].
The following screen appears:
Automation Config
Auto Resume Off
The Auto Program / Auto Resume screen provides the option for an autosampler program
to automatically resume where it left off (by selecting Auto) should a power failure occur.
To select the Auto Resume option:
Press [On/Yes 1], then press [Enter].
Upon powerup, the Clarus GC sets up the method that was running when the power was lost
and runs it one time without injecting a sample. If any automation sequence was
interrupted, it is resumed.
7. Press [Status Escape] to return to the System Control menu or press [Enter] to display
the Oven Maximum Temperature Limit screen.
55
Configuring the Oven

Configuring the oven consists of setting the oven maximum temperature limit, calibrating the
oven, and setting an oven equilibration time. It is good practice to set the oven maximum
temperature limit to a value that will protect your column from high temperatures. Refer to
your column data sheets for the column maximum temperature value.
To configure the oven:
1. If necessary, display the Oven Maximum Temperature Limit screen by pressing
[System] [Enter] [Oven Prog].
The Oven Maximum Temperature Limit screen appears:
Oven Maximum Config
Temp Limit 450
2. Type a value for the maximum allowable oven temperature, then press [Enter] or accept
the displayed value by pressing [Enter].
The Oven Temperature Calibrate screen appears:
Oven Temp
Calibrate ?
Config
No
3. If you wish to calibrate, press [Yes/ 1] [Enter] "Calibrating the Oven Temperature," in
Chapter 13 otherwise press [No / 0] [Enter].
The Oven Equilibration Time screen appears:
Oven
Config
Equil. Time 2.0 m
The oven equilibration time is the amount of time you wish to equilibrate the oven at the
current temperature after it had cooled down or changed from the initial temperature.
The default value is 2.0 minutes.
4. Type an equilibration time (in minutes), then press [Enter].
the next configuration screen.
56
Configuring a Sleep Time

Sleep time is the length of idle time in minutes (that you set) before the GC automatically sets
up the sleep method. The sleep method is a GC method which you designed and stored.
When run, the sleep method shuts down the Clarus GC in a way that protects the column.
CAUTION
If the display shows Sleep Mode do not activate this mode

since this function is only available in the PPC option. The
PPC option is not available on the Clarus 400/480 GC. If
you inadvertently select this option, reboot the Clarus GC.
Once the instrument is rebooted select the Config screen
and switch off the Sleep Mode so the Clarus GC will
function properly
How Sleep Works
After the Clarus GC is idle with no keyboard or chromatographic activity for a period of time
longer than the specified sleep time, the sleep method automatically sets up. The Clarus GC
top level status screen displays with a status of SLEEP instead of READY with the sleep
method number displayed as the active method number.
While running the sleep method, the [Run] key is inactive and the GC is NOT READY to any
interconnected devices such as data handling systems. To exit the sleep mode, set up a new
method or start an automated analysis.
To define a sleep time:
1. Copy or generate and then save a method to an unused method number, for example,
Method 3. Then edit that method by entering the parameters for a sleep condition.
2. If necessary, display the Sleep Time screen by pressing [System] [Enter] [Oven Prog]
[Enter] [Enter] [Enter].
The Sleep Time screen appears:
Sleep Time
Set
Config
Off
3. Type a sleep time value between 5 and 999 minutes (typing a 0 turns off the sleep
mode). Then press [Enter].
57
The Sleep Method screen appears:

Sleep Method
1 2 3
5
Config
The Sleep Method screen contains the numbers of the saved methods. The above screen
shows that methods 1, 2, 3, and 5 are saved.
4. Select a sleep method from the available stored GC methods in memory. For example, since
you saved the sleep method as Method 3, select Method 3. Then press [Enter].
the Heating Delay screen.
58
Setting an Oven Heating Delay

To avoid detector condensation and contamination, it is good practice to delay heating the oven
until the gas flows and detector temperatures are ready. We typically set the heating delay Off,
which means that the oven begins to heat to the set temperature the moment you turn on the
GC. However, to delay heating the oven until the detectors reach the set temperature, you can
set the oven heating delay ON.
To set an oven heating delay:
1. If necessary, display the Heating Delay screen by pressing [System] [Enter] [Time]
[Time] [Time].
The Heating Delay screen appears.
Heating Delay Config
Set
Off
2. If you wish to set an oven heating delay, press [On / 1]. If you do not wish to set an oven
heating delay, press [Off / 0].
3. After setting on or off, press [Enter] to accept the selection, then press [Enter] again to
display the Time of Day Set Clock screen or press [Status Escape] to return to the
System Control menu.
59
Setting the Real Time Clock and Startup Time

You can use the Startup Time to automatically set up the Clarus GC with a specified method
that allows time for equilibration and conditioning prior to the start of the analysis.
To set the real time clock and startup time:
1. If necessary, display the Time of Day Set Clock screen by pressing [System] [Enter]
[Time] [Enter] [Enter] [Enter].
The Time of Day Set Clock screen appears:
Time of Day
Set Clock?
Config
Yes
2. If you wish to set the clock, press [Yes / 1] [Enter].

A screen similar to the following appears:
Min:
00:
Hr:
00:
Dy:
00:
Mo:
00:
Yr:
00
3. Press [->Set] to move the cursor to each of the positions, then enter the correct value for
each parameter. The hours (Hr) range is 1-24. After typing the year (Yr), press [Enter]
to accept the setting.
The Startup Time screen appears:
Startup Time
Set a time?
Config
No
4. If you wish to set a startup time, press [Yes / 1] [Enter].

Min:
00:
Hr:
00:
Dy:
00:
Mo:
00:
Yr:
00
5. Press [->Set] to move the cursor to each position, then enter the correct value for each
parameter. The hours range is 1-24. After typing the year, press [Enter] to accept the
setting. After typing the year, press [Enter] to accept the setting, then press [Enter].
The following screen appears with the available methods that you have created and stored
(saved):
60
StartUp
1
Meth Config
5
6. Press [->Set] to select startup method, then press [Enter].

StartUp
Once
Rept
Config
Always
7. Press [->Set] to select your choice, then press [Enter] to accept the value. Press [Status
Escape] to return to the System Control menu.
61
Configuring an Injector
Your Clarus GC is configured for the installed injectors at the factory; however, if you need
to view or change the injector configuration follow this procedure.
To configure an injector:
1. Press [System] [Enter] [Inject Prog].
The first injector configuration screen appears:
Injector 1
Config
None Pkd Cap GSV >
The position of the cursor tells you the type of injector installed in position 1. The above
screen shows that a capillary injector is installed in position 1.
2. To change the injector configuration, press the [->Set] key the number of times necessary to
select the type of injector you want to configure for position 1.
3. Press [Enter].
4. Press [Enter].
HEADSPACE
Installed?
Config
No
If Headspace is installed in your system, press [Yes/ 1] and the following screen appears:
HS40
Car1 Car2
Config
Both
Press [->Set] to select where Headspace is installed and press [Enter].

5. Press [Enter] to display the carrier gas configuration screen or press [Status Escape] to
return to the main menu
62
Configuring Carrier Gas Operation

Your Clarus GC has been configured at the factory for the installed injectors and detectors.
However, you must complete some parts of this configuration before you can run an analysis.
The following procedures show how to configure the carrier gas manual pneumatics operation.
Upon initial startup, the Clarus GC monitors the carrier gas inlet pressure. If this pressure is
less than 50 psi, the following message occurs.
Warning: Car1 Inlet
< 50 psi, Press CE
After you press CE, this message will not occur again, even if you did not correct the
situation.
Configuring the Carrier Gas Operation

Configuring the Carrier Gas for Capillary Inlets
To configure the carrier gas for capillary follow this procedure:
1. Press [System] [Enter] [Carrier Prog].
The Gas Display screen appears:
Gas Display
None
kPa
Note:
1 Config
PSIG Flow
The optional readout was configured before shipment from the factory.
2. Press the [->Set] key two times to move the cursor to the left of PSIG, if it is not already
there and press [Enter].
3. You can press [Enter] proceed to configure valves or press [Status Escape] to return to
the main screen.
Configuring the Carrier Gas for Packed Inlets
1. Press [System] [Enter] [Carrier Prog].
The Gas Display screen appears:
63
Gas Display 1
None kPa
Note:
Config
PSIG Flow
The optional readout was configured before shipment from the factory.
2. Press the [->Set] key three times to move the cursor to the left of Flow, if it is not already
there.
3. Press [Enter] and a screen similar to the following appears:
Carrier
He
Gas 1
N2 H2
Config
Ar/Ch4
4. Move the cursor with the [->Set] key to the left of the carrier gas you are using, then
press [Enter]. If you are using helium, just press [Enter].
Carrier Gas 1
Calibrate Flow ?
Config
No
5. Select [Yes], then press [Enter] and the following appears:

Calib Flow 1
Lo=0
Note:
He
Hi=100
The optional Flow Readout is calibrated in the factory using Helium carrier gas. If you are
using a carrier gas other than Helium, you must select the gas as shown in the above
example. You do not have to recalibrate.
If you install a 0-20 mL/min flow element, you must recalibrate. Refer to Calibrating the
Flow Readout, Chapter 9 for this procedure.
6. Press [Enter] to display the Carrier Gas 2 Config screen or press [Status Escape] to
return to the main menu.
64
Configuring Valves
To configure a valve:
Method 1
READY
35
1. Press [System] [Enter] [Valve].

Valve 1
Config
Split
Split is the only choice for Valve 1.
2. Press [Enter].
Valve 2
Config
Split
Split is the choice for Valve 2 since a capillary injector is configured for Injector 2.
3. Press [Enter].
Valve 3
Config
None Valv Split GSV
Since Valve 3 has not been configured for anything at this time all selections are
available
4. Press [Enter] and continue to view or configure Valves 4, 5, and 6.
5. Press [Enter] to display the Detector 1 Configuration screen or press [Status Escape]
to return to the main menu.
65
Configuring Detectors
Determining the Number, Type, and Position of Installed Detectors
This procedure describes how to configure detectors using a typical example: an FID in
position 1 and an ECD in position 2:
1. If necessary, press [System][Enter][Detect Control].
If a detector is installed in position 1, an appropriate screen appears. For example, if a
FID is installed in position 1, the following screen appears:
Detector 1
FID
Config
Output
2. Press [Enter].
The FID Filter screen appears:
FID 1 Filter
50 200
Config
800
The default setting is 200 milliseconds. If you want to improve the signal-to-noise,
change the setting to 800 milliseconds. The noise improves, but the peak shapes broaden.
A setting of 50 gives a faster detector response, but it may increase the noise level.
3. Press [->Set] to select a filter value, then press [Enter].
The FID Flameout detection screen appears:
FID 1
Flameout
Note:
Config
0.3 mV
You must set a Flameout value in millivolts (mV) for the FID auto-ignition feature to work.
For example, 0.3 mV.
Flameout detection occurs 0.5 minutes into the PRE-RUN time and it measures the userentered baseline threshold level in mV. In this example 0.3 mV are used. If the 0.3 mV
threshold level is exceeded, the flame is considered lit; otherwise, the auto-ignite sequence
begins to automatically ignite the flame.
4. Type a flameout detection level in mV (for example, 0.3 mV) and press [Enter] to accept
the entry. Press [Enter] again to display the next screen.
66
The screen to set the air flow (Air Set) appears. The actual flow is on the top line and the
setpoint flow value is to the right of the cursor on the bottom line.
FID 1
0
Air
Set 0 mL
Type 450 to set the FID 1 air flow to 450 mL/min then press [Enter].
5. Press [Enter].
The screen to set the hydrogen flow (H2 Set) appears. The actual flow is on the top line
and the setpoint flow is on the bottom line.
FID 1
H2
0
Set 0 mL
Type 45 to set the FID 1 hydrogen to 45 mL/min then press [Enter].

6. Press [Enter].
If an ECD is installed in channel 2, an appropriate screen appears, for example:
Detector 2 Config
ECD
Output
7. Pressing [Detect Control] again displays the AUX heated zone configuration with the
following choices:
Aux
Config
None AUX
If a single TCD is installed, the AUX zone choices are:
Aux
Config
None AUX TCD
Notice that TCD is the default setting.
If dual TCDs are installed, the AUX zone choices are:
Aux
None
Config
AUX
Notice that None is the default setting.
67
CAUTION
If your Clarus GC has dual TCDs installed or a single TCD

installed but not configured for the AUX zone, then it is not
recommended to temperature programming the GC oven.
8. Press [Enter] to display the detector gas flow screen or press [Status Escape] to return to
the main menu.
68
Configuring a Recorder and/or Integrator

The Clarus GC comes equipped with up to two output channels, one for each installed
detector. Two menus allow you to specify whether you attached a recorder or integrator to
the Detector 1 or Detector 2 output channels during installation of the Clarus.
To see the menu for Output 1 if the detector 1 amplifier is plugged in:
1. Press [System] [Enter] [Output].
Output 1 Config
Recorder Integrator
The number on the top line refers to the output channel corresponding to detector position
1.
If a recorder is attached, the detector output is set for a 1 mV recorder.
If an integrator is attached, the detector output range is 0 to 1 Volt.
If a recorder is attached to output 1, press [Enter].
If an integrator is attached to output 1, press [->Set] [Enter].
In either case the Output 2 screen appears, but only if a detector has been installed in
position 2 (rear).
Output 2
Recorder
Config
Integrator
2. Configure a recorder or integrator for Output 2 using the same procedure as for Output 1.
3. Press [Enter] to display the Integrator 1 Configuration Offset screen or press [Status
Escape] to return to the main menu.
69
Configuring Integrator/Recorder Offsets

Offset is the signal level that appears at the analog output when you set the detector autozero
On in the Active Method. The default offset values are satisfactory for most applications.
To change offsets:
1. If necessary, press [System] [Enter] [Auto Zero].
If you configured Output 1 as an integrator, the following appears:
Int 1
Offset
Config
5.0 mV
If you configured Output 1 as a recorder, the Offset parameter screen appears as shown
below:
Rec 1
Offset
Note:
Config
5%
Integrator offset is expressed in millivolts whereas recorder offset is expressed as a

percentage of full scale of a 1 mV recorder.
to return to the System Control menu.
To change an offset value for Output 1 above:
1. Type the new value, then press [Enter]. The Offset screen for Output 2 appears (but only
if a device has been configured for this output channel).
Rec 2
Offset
Config
5%
to return to the System Control menu.
To change an offset value for Output 2 above:
1. Type in the new value, then press [Enter].
Note:
The offset values are not applied to the digital computer signal; they are only applied to the
analog outputs.
2. Press [Enter] to display the initial Automation Configure screen or press [Status
Escape] to return to the main menu.
70
Configuring a Printer
The print options that are displayed on various menus do not appear unless a printer is
configured.
To configure a printer:
1. If necessary, press [System] [System].
Page 2 of the System Control menu appears:
System
Control
Stpwtch Extern >
2. Press [->Set] [Enter].
External Device
None Printer Cmptr
3. Select Printer and press [Enter].
Printer Baud
3 12
24
Note:
X1
48
00
96
The values in the above menu and those below are default values for most serial printers.
Check the manual supplied with your printer and make the required changes.
4. Press [Enter].
Printer
Data
7
Bits
8
5. Press [Enter].
Printer
Even
Parity
Odd
None
6. Press [Enter].
71
Printer
1
Stop
2
Bits
7. Press [Enter].
8. Press [Status Escape] to return to the System Control menu.
72
Setting Up
Detectors
74
About this Chapter

This chapter contains procedures for setting up the following detectors:
FID (flame ionization)
TCD (thermal conductivity)
ECD (electron capture)
NPD (nitrogen phosphorus)
The instructions provided in this chapter describe how to set detector gases that are
controlled by needle valves and pressure regulators (also known as manual pneumatics).
The instructional procedures in this chapter are written with the assumption that:
You know how to measure gas flows using a flowmeter with the Clarus GCs
built-in stopwatch. If not, prior to continuing, please read "Using the Built-in
Stopwatch" in Chapter 4, "Before You Install a Column."
All heaters are turned OFF and cool to the touch.
WARNING
Note:
The instant the Clarus GC is turned on, the oven, injector(s), and
detector(s) begin to heat up rapidly. To avoid injury, turn off all
heaters and allow their respective zones to become cool to the touch
before you touch detectors, injectors, and their corresponding fittings.
Detailed procedures for turning heaters off and on are in Chapter 3,
"Before you Install a Column" In the Clarus 400/480 GC Hardware
Guide. If you have not read Chapter 3, please do so before
proceeding.
A column has been installed, carrier gas flow or pressure has been set, and all
connections have been leak tested.
not supported by the Clarus GC. Please ignore these functions and continue with your
analysis.
75
Setting Up Detectors
Setting up a FID
WARNING
Do not turn on the hydrogen until you verify that a column is

connected to the detector fitting inside the oven and all connections
have been leak tested. The Flame Ionization Detector (FID) uses
hydrogen as fuel. If you turn on the hydrogen without a column
connected to the detector fitting inside the oven, hydrogen could
diffuse into the oven creating the possibility for an explosion.
Before disconnecting a column, make certain that the hydrogen has
been turned OFF.
If two FIDs are installed, but only one FID has a column connected
to it, you must plug the unused FID inlet fitting with a 1/8-inch
stainless steel plug (P/N N930-0061).
The detector gas modules have been set to OFF at the factory.
CAUTION
76
FID Overview
Flame Ionization Detectors (FID) are mass sensitive and used for the destructive analysis
of organic compounds.
As the sample enters the detector, it is mixed with hydrogen and then burned in air,
thereby generating ions. The ions are collected and measured by the detector, with their
concentration proportional to the amount of compound present. Ion collection is
enhanced by a polarized electric field that is created by applying a negative voltage (200
V) to the jet tip. The detector sensitivity is affected primarily by the hydrogen flow.
A cross section view of a FID is shown below.
Amplifier
Connector
Ignitor
Polarizing Pin
Collector
Flame Jet
Air In
Hydrogen In
Flame Jet
Extension
Detector
Fitting
Figure 11 Flame Ionization Detector (FID).
77
Setting Up a Manual Pneumatics FID

To set up the manual pneumatics version of the FID, read the FID Setup Summary and
follow the steps.
FID Setup Summary

To set up the manual pneumatics version of the FID:
1. Connect a flowmeter to the FID outlet.
2. Adjust the hydrogen flow.
3. Adjust the air flow.
4. Ignite the flame.
1.
Connect a Flowmeter to the FID Collector
1. Open the detector cover shown in Figure 12.

This exposes the detector outlets. Figure 13 shows a top view of the FID outlet.
78
Detector Cover
Figure 12. Location of the detector cover.
79
2. Insert the end of the flowmeter tubing into the FID adapter (P/N N610-3119,
supplied in the shipping kit). Then insert the adapter into the FID collector.
See the following figure.
Tubing from the flowmeter

Adapter
(P/N N610-3119)
FID Collector
Figure 13 Connecting the flowmeter to the FID collector.
2.
Adjust the Hydrogen Flow
To adjust the combustion gases, the manual pneumatics consist of an on/off needle valve
for air and on/off regulator for hydrogen mounted on the pneumatics control panel.
CAUTION
80
Do not overtighten the inner flow adjustment screw in the on/off

needle valve or the on/off regulator. Overtightening damages the
mechanical device.
AIR
Figure 14 Combustion gas control valves for a manual pneumatics FID.

Each pneumatic control consists of an outer knob (which is used to turn the hydrogen or
air completely on or off), a cap, and an inner gas flow adjustment screw.
Removing the cap exposes the gas flow adjustment screw. To set the air, flow use a small
thin screwdriver (P/N 0990-7273, supplied in the shipping kit) to turn the adjustment
screw. Turn the screwdriver counterclockwise to increase the flow or clockwise to
decrease the flow. To set the hydrogen, use a hex wrench (P/N 0990-7235, supplied in the
shipping kit) to turn the adjustment screw. Turn the hex wrench clockwise to increase the
flow or counterclockwise to decrease the flow.
To adjust the hydrogen flow:
1. Turn the air off by turning the outer ring of the air control valve completely
clockwise.
2. Turn on the hydrogen at the tank. Adjust the line pressure to 30 psig.
3. Start the hydrogen flowing by turning the outer ring of the hydrogen pressure
regulator completely counterclockwise (see Figure 14).
81
CAUTION
The outer knob is the on/off knob and it must be turned fully on for
complete flow. In the case of the pressure regulator, if this knob is
only partially opened, the flow will be less than the setting made
when the knob was fully opened.
4. To access the adjustment screw, remove the protective cap from the hydrogen
pressure regulator.
5. Insert the hex wrench (P/N 0990-7235) in the adjustment screw and turn it clockwise a
few turns.
For safety reasons, the hydrogen pressure regulator is set to a very low flow before it
is shipped from the factory.
6. Display the Stopwatch screen by pressing [System] [System] [Enter].
Stopwatch
0.00 min
Flow
Vol 1
7. Measure the flow rate.

For best accuracy, use a soap bubble flowmeter volume that gives a reading of at
least 30 seconds.
Note:
All gases exit through the top of the FID. If you use a flowmeter to measure the air and
hydrogen gas flows with a column connected to the FID and the carrier gas flowing,
remember to subtract the carrier gas flow from the total measured flow.
8. Repeatedly adjust the hydrogen flow and measure the flow until you obtain a flow
rate of about 45 mL/min.
Note:
Both the carrier gas and hydrogen gas exit through the FID. For satisfactory operation
of the FID, a flow rate of 45 mL/min of hydrogen is required. If a column is connected to
the FID, and the carrier gas is set and flowing, you should add the carrier gas flow rate
to the required hydrogen flow. For example, if the carrier gas flow is 30 mL/min, adjust
the hydrogen flow until the measured total flow rate (combined carrier gas and
hydrogen) is about 75 mL/min (45 mL/min of hydrogen plus 30 mL/min of carrier gas).
9. Turn off the hydrogen flow by turning the outer ring of the hydrogen control valve
completely clockwise.
82
10. Replace the protective cap on the hydrogen pressure regulator.
3.
Adjust the Air Flow
1. Turn on the air at the source. Adjust the line pressure to 30 psig.
2. Make certain that the flowmeter is still attached to the FID collector.
3. Start the air flowing by turning the outer ring of the air control valve (see Figure 14)
fully counterclockwise.
4. Remove the protective cap from the air control valve.
The stopwatch screen should still be displayed.
least 30 seconds.
6. Repeatedly adjust the air flow by turning the needle valve with a small screwdriver
(P/N 0990-7273) and measure the flow until you achieve a flow rate of about 450
mL/min.
Note:
Both the carrier gas and air exit through the FID. For satisfactory operation of the FID,
a flow rate of 450 mL/ min of air is required. If a column is being used with the FID, and
the carrier gas has been set and is flowing, the carrier gas flow rate should be added to
the required air flow. For example, if the carrier gas flow is 30 mL/min, adjust the air
flow until the measured total flow rate (combined carrier gas and air) is about 480
mL/min.
7. Turn off the air flow by turning the outer ring of the air control valve completely
clockwise.
8. Replace the air control valve protective cap, remove the flowmeter, and replace the
FID cap.
9. Press [Status Escape].
83
CAUTION
4.
If at any time the line pressure is changed from 30 psig, you must
remeasure and adjust the air flows.
Ignite the Flame
1. Press [Detect Control] until the appropriate FID Temperature screen appears:
FID 1
NOT RDY
Temperature
Note:
35
100
For proper ignition to occur, the FID must be heated to at least 100 C.
2. Enter a setpoint of at least 100 C, or enter a value 50 C higher than the highest
temperature of your oven program.
3. Close the oven door. Wait for the FID 1 temperature to become READY:
FID 1
READY
Temperature
100
100
4. Turn on the hydrogen by turning the outer knob of the hydrogen pressure regulator
valve fully counterclockwise.
CAUTION
5. After purging the FID with hydrogen for a minimum of 60 seconds, press [Detect
Control] once or twice until your FID is displayed. Then press [Enter]. The
(Note the signal level in mV before the flame ignites.)
84
FID 1 Signal
0.00 mV
Push Set to Ignite
6. Press the [->Set] key.
Method
System
Auto
BackGround
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
Run
0 no
Figure 15 Location of the Set key.

Upon pressing the [->Set] key, observe the glow plug glowing on top of the FID
collector.
6. Quickly turn the air on by turning the outer knob of the air control valve fully
counterclockwise.
85
Glow Plug Ignitor
Figure 16 Location of the glow plug.

When you hear a "POP, observe the Signal level in mV as it increases on the
screen and remains greater than the previously noted amount.
FID 1 Signal 0.52 mV
Flame Ignition 1
86
After the flame is lit, the following screen appears:

FID 1 A/Z
Initial
0.05mV
on
The signal level shown in this screen is at the range that you set so if you have set a
range of 10, the signal will be 10 times smaller.
You can also confirm that the flame is lit by holding a shiny object (such as a mirror
or small wrench) over the FID outlet. Condensation will appear on the object if
ignition has occurred.
The FID outlet is hot! To prevent injury, never place your hand over
the FID outlet.
WARNING
If the Flame Goes Out During a Run

If the flame goes out during a run, the run continues until completion but the data is
obviously bad. When the Clarus prepares for the next run it, checks for a flame by
running the Flameout test. If the Clarus detects that the flame is out, the following
screen appears.
Failed to ignite
flame, Press CE
You must then manually ignite the flame.
CAUTION
To prevent condensation from forming on the FID, always turn off

the flame (both hydrogen and air gases) before cooling the detector
or turning off the Clarus GC.
87
Using the FID in Corrosive Environments

If you are analyzing samples (such as chloroform, methylene chloride, etc.), that produce
corrosive by-products, we recommend installing the piece of vent tubing (P/N 02506490) supplied in the Clarus 400/480 GC Shipping Kit (P/N N6100348) and setting the
FID temperature greater than 250 C to minimize condensation from forming. Since
these corrosive by-products attack the top of the FID collector assembly, including the
ignitor, we strongly recommend venting the FID into a vent hood.
CAUTION
The flame will not ignite with this vent tubing installed. To ignite
the flame, you must first remove the vent tubing, ignite the flame,
and then replace the vent tubing.
To install the vent tubing:

1. Ignite the FID flame.
The FID outlet is hot! To prevent injury, never place your hand over
the FID outlet.
WARNING
2. Lift open the detector cover.

3. Cut the piece of tubing (P/N 0250-6490) to a length of 4-inches and firmly insert one
end of the tubing into the top of the FID.
4. Route the end of the tubing through the hole in the detector cover as you close the
detector cover.
5. Connect one end of a length of vent tubing to this piece of tubing and place the other
end in a vent hood.
88
Setting up an ECD
WARNING
To assure that removable radioactive contamination on the external

parts of the ECD remain at a safe level, the United States Nuclear
Regulatory Commission requires that:
the ECD is Wipe Tested at least once every six months and
a record of the results are maintained for NRC inspection.
Please refer to Chapter 7, Maintenance in the Clarus 400/480 GC
Hardware Guide, for the Wipe Test procedure.
CAUTION
THERMAL RUNAWAY PROTECTION: The Clarus GC

software shuts down the GC if any heated zone exceeds 470 C.
Should this occur, the following error message is displayed:
INSTRUMENT SHUTDOWN
xxxxx THERM RUNAWAY
....where xxxxx is the heated zone.
Call your PerkinElmer Representative.

Instrument shutdown also occurs if there is a PRT (Platinum
Resistance Thermometer) or MPU (Micro Processor Unit) failure.
In these cases the following error message is displayed:
INSTRUMENT SHUTDOWN
xxxxx PRT ERROR
....where xxxxx is the failed zone.
Call your PerkinElmer Representative.
The detector gas modules have been set to OFF at the factor.
CAUTION
89
United States Government Regulations for ECDs
CAUTION
Repairing an Electron Capture Detector cell requires a specific

license by the U.S. Nuclear Regulatory Commission (NRC) and/or
in some states by the equivalent state agency. For further
information on obtaining a license, contact PerkinElmer, 710
Bridgeport Ave, Shelton, CT 06484, Connecticut Customer Service
department or the NRC Material Branch Office of Nuclear
Materials, Safety and Safeguards, Washington, DC 20555.
Special Instructions for ECD Cell Purchasers

(Who are not Specifically Licensed to Handle Radioactive
Materials)
The PerkinElmer Electron Capture Detector (P/N N610-0063, 120 V or N610-0134, 230
V) contains 15 mCi of Nickel-63 (Ni 63), a radioactive material. Your possession and
use of this detector is governed by 10 C.F.R. Section 31.5, which is reproduced in
Appendix I. Under the provisions of that regulation you are deemed a "General
Licensee."
Your possession and use of the Detector Cell may also be regulated by the state where
you are located. The requirements of state regulatory agencies are substantially similar to
those contained in NRC regulation 10 C.F.R. Section 31.5, but they may differ in some
respects. It is suggested that you procure a copy of the regulations of your particular
state. (Supplement 2 in Appendix I contains a list of the "Agreement States" which have
been granted authority by the U.S. Nuclear Regulatory Commission to regulate the
possession and use of radioactive material.)
It is required that you are familiar with regulation 10 C.F.R. Section 31.5 (Supplement 1).
Following are summaries of its requirements.
Labels
Do not remove any of the labels attached to the ECD cell or any of the labels attached to
your Clarus GC that refer to the ECD cell. Follow all instructions and abide by all
precautions provided by the labels and in user instruction manuals referred to by the
labels.
90
Leak Testing
You are obligated under federal and state regulations to make certain that the ECD cell is
wipe tested for leakage of radioactive materials at intervals of no longer than six months,
and that the analysis of these wipe tests is conducted by a person specifically licensed to
do so, either by the U.S. Nuclear Regulatory Commission or by an Agreement State. The
analyses can be performed by the firm listed below:
National Leak Test Center
P.O. Box 486
North Tonawanda, New York 14120
Cell Failure or Damage
If a leak test detects more than 0.005 mCi of removable radioactive material on the surface
of an ECD cell, or if the cell itself is damaged in such a way as to indicate that it may no
longer adequately shield the radioactive material inside, you must immediately suspend
operation of your chromatograph until the cell has been repaired or disposed of by a person
specifically licensed to do so. Any such incident must be reported by you to the Regional
Office, Inspection and Enforcement, U.S. Nuclear Regulatory Commission.
Reporting Radiation Incidents, Theft or Loss
Please read NRC Regulation 10 C.F.R. Section 20.402 and 20.403 (see the Appendix in
the Clarus 400/480 GC Hardware Guide). These describe your duties should the
radioactive material (Ni 63) in the ECD cell be lost, stolen, or released, or should any
person be exposed to radiation.
Other Requirements
Regulation 10 C.F.R. Section 31.5 (see the Appendix in the Clarus 400/480 GC Hardware
Guide) does not permit you to abandon the ECD cell or export it. It may not be transferred
except to a person specifically licensed to receive it. Within thirty days of such a transfer,
you must report to the Director of Nuclear Material Safety and Safeguards, U.S. Nuclear
Regulatory Commission, Washington, D.C. 20555, the name and address of the transferee.
However, no report is needed to transfer a used or defective ECD cell to PerkinElmer in
order to obtain a replacement. You may transfer the ECD cell to another general licensee,
like yourself, only when it remains at the same location to which it was shipped by
PerkinElmer. Give the transferee a copy of these instructions and the regulations in
Appendix I, and report to the commission as required in Regulation C.F.R. Section 31.5.
91
The ECD cell may only be removed for repair from the
chromatograph if a specific license has been obtained, THE CELL
SHOULD NEVER BE DISMANTLED.
WARNING
United Kingdom Regulations

In the U.K., registration is required under the Radioactive Substances Act of 1960, for
anyone keeping or using radioactive materials. Application should be made to any one of
the following governing bodies:
ENGLAND
Department of the Environment Queen Anne's Chambers

Tothill Street
London, SW1H 9J4
SCOTLAND
Scottish Development Department

21 Hill Street
Edinburgh, EH2 3J4
WALES
Welsh Office
Cathay's Park
Cardiff, CF1 3NG
NORTHERN
IRELAND
Ministry of Development
Parliament Building
Storemont
Belfast, Northern Ireland
92
ECD Overview
The Electron Capture Detector (ECD) is the most sensitive detector available for the analysis
of electrophilic compounds such as chlorinated hydrocarbons found in pesticide residues. It
is concentration-sensitive and nondestructive.
The ECD cell contains a nickel foil in a cylinder through which the carrier gas flows. The
coating of the foil's inner surface contains the radioactive isotope Nickel-63 and has a
nominal sensitivity of 15 mCi. To optimize detector response, make-up gas is combined
with column effluent.
Beta particles emitted from the isotope ionize the carrier gas. The resultant ions and
electrons travel to the collector anode assembly under the influence of a pulsed polarizing
voltage applied between the source and the collector. The pulse frequency is varied to
maintain a constant average current. The presence of an electron absorbing species in the
detector decreases the current as the absorbed electrons form ions, which travel more slowly
than electrons. The pulse frequency of the polarizing supply is automatically controlled to
maintain a constant current and is used to form the detector output signal.
The ECD works with nitrogen carrier or makeup gas or a carrier or makeup gas mixture
of 95% argon/5% methane. When using capillary columns at low flows (5 mL/min or
less), helium or hydrogen may be used as the carrier gas provided nitrogen or
argon/methane is used as the make-up gas. A cross section view of an ECD is shown
below.
93
Collector (Anode)
To Amplifier
63
Ni Foil (Source)
Makeup Gas In
Column Connection
Figure 17 Electron Capture Detector (ECD).

If you are using the ECD with a packed column, check to see whether the optional Flow
Readout was calibrated with nitrogen or argon/methane carrier gas. If not, select the
appropriate carrier gas (see Chapter 9, System Utilities).
To function properly, the total carrier gas flow through the detector should be 30 mL/min
or more. Where required, the total carrier gas flow is adjusted to this value with make-up
gas using the make-up gas control valve located on the pneumatics control panel. The
appearance and location of the make-up gas control valve is shown in Figure 8-12.
Note:
If you want to switch between a FID and an ECD, when using the same packed column
injector, use nitrogen as the carrier gas for both detectors. Argon/methane is not
recommended for use with an FID because it produces a high background, more noise,
and a wandering baseline.
94
CAUTION
CAUTION
To minimize detector contamination, run the ECD hot, at a

temperature of at least 375 C.
You may experience high background readings when working with

capillary columns. The high background may be caused by liquid
phase bleeding off the detector end of the column (at a typical
temperature of 375 C or higher). In some cases the polyimide
coating of the column may also cause a high background reading
when using the ECD.
You can correct this situation by installing a glass-lined receiver
(P/N N600-0968). The glass-lined receiver terminates in a 1/16inch fitting so that it can accept capillary columns with an i.d. of
530 microns or less.
If you suspect that the background is caused by column liquid
phase bleeding, install the glass-lined receiver in the detector base.
Then insert the column end just beyond the ferrule and connect it to
the receiver.
If you suspect that the background is caused by the polyimide,
insert the column through the glass-lined receiver until it is flush
with the end of the receiver. Then insert the receiver into the
detector base. This shields the column from the make-up gas flow.
95
Setting Up an ECD
To set up a ECD, read the ECD setup summary, then follow the steps.
ECD Setup Summary

To set up an ECD:
1. Vent the ECD outlet.
2. Adjust the make-up gas flow.
CAUTION
1.
Because an ECD is extremely sensitive, contamination from any

part of the system can add to the background and noise. To help
assure a clean system the injector and detector should be baked-out
and both packed and capillary columns thoroughly conditioned
before use. When conditioning columns for use with an ECD, DO
NOT attach the column to the ECD. Clean tubing and pure filtered
gases should be used. Whenever a column is disconnected from an
ECD, the ECD should first be cooled to avoid oxidation of the
Nickel foil.
Vent the ECD Outlet
CAUTION
If venting the ECD effluent is required, attach an additional piece

of tubing to the tubing that is connected to the ECD outlet. This
does not affect the performance of the ECD.
1. Open the detector cover (see the following figure) to expose the top of the ECD.
96
Insulating Cover
Detector Cap
Screw
Screw
Figure 18 Top view of an ECD.

2. Remove the two screws that secure the insulating cover to the Clarus GC.
3. Remove the insulating cover and detector cap. This exposes the ECD outlet (see the
following figure).
4. Attach the outer metal sleeve of the vent tubing (P/N N610-0161) to the ECD Outlet.
97
Vent Tubing
ECD Outlet
Figure 19 Connecting vent tubing to the ECD outlet.

5. Press down and turn the metal sleeve on the end of the vent tubing to
secure it to the ECD.
6. Thread the vent tubing through the detector cap and insulating cover as you position
them over the ECD.
7. Secure the insulating cover to the Clarus GC with the two screws previously
removed.
8. Thread the tubing through hole in the detector cover then close the detector cover.
This hole is either directly above the ECD or at the rear of the detector cover,
depending on the detector configuration.
9. Attach a flowmeter to the vent tubing.
98
2.
Adjust the Make-up Gas Flow
The following procedures describe how to set the make-up gas in the Clarus GC.
CAUTION
The ECD flow module for make-up gas is calibrated with nitrogen
gas at the factory. You must recalibrate the ECD flow module if
you are using a make-up gas other than nitrogen.
Adjust the Make-Up Gas in the Manual Pneumatics

To adjust the make-up gas in the manual pneumatics version, use the on/off needle valve
mounted on the pneumatics control panel.
CAUTION
Do not overtighten the inner flow adjustment screw in the on/off

needle valve or the on/off regulator. Overtightening damages the
mechanical device.
ECD Make-Up
Figure 20. The ECD make-up gas control valve for an ECD.
99
The make-up gas control valve consists of an outer ring (used to turn the make-up gas
completely off or on), a protective cap, and an inner needle valve (used to adjust the flow
of make-up gas). Removing the cap exposes the needle valve adjustment screw. To set
flow, use a small thin screwdriver (P/N 0990-7273, supplied in the shipping kit) to turn
the adjustment screw. Turn the screwdriver counterclockwise to increase the flow or
clockwise to decrease the flow.
You should only adjust make-up gas flow after a column has been installed and the
carrier gas flow or pressure has been set to the value required for the analysis.
Make-up gas need not be added when using packed columns, where the carrier gas flow
is 30 mL/min or higher.
To adjust the make-up gas:
1. Turn the outer ring of the make-up valve fully clockwise.
2. Display the built-in stopwatch by pressing [System] [System] [Enter].
3. Measure the column flow rate and make certain that it is set to the desired value.
least 30 seconds.
4. Turn the outer ring of the make-up valve fully counterclockwise.
5. Remove the protective cap from the make-up valve.
6. Repeatedly adjust the make-up gas (turn the needle valve using the screwdriver (P/N
0990-7273) counterclockwise to increase the flow, clockwise to decrease the flow).
Adjust the total flow until it equals 30 mL/min or higher.
Note:
The lower the total flow, the better the sensitivity, provided that peak shape is
maintained.
7. Replace the cap on the make-up gas valve and disconnect the flowmeter.
100
Setting Up a TCD
CAUTION
TCD Overview
The Thermal Conductivity Detector (TCD) is a dual-channel detector which measures the
difference in thermal conductivity between carrier gas flowing through a reference
channel and carrier gas plus sample flowing through an analytical channel (see the
following figure).
Four tungsten-rhenium filaments are connected in a bridge circuit, two in each channel.
The TCD is set up with the same amount of carrier gas flowing through both channels.
The presence of a sample component in the carrier gas flowing through the analytical
channel changes the resistance of the filaments in that channel. This unbalances the
bridge and produces a signal proportional to the amount of sample.
Reference Out
Reference In
Carrier Out
Carrier In
Figure 21. Thermal Conductivity Detector (TCD).

101
Setting Up a TCD
Setting up a TCD requires that you equalize carrier gas flows through both channels,
followed by balancing the current through the two filaments. The TCD is nondestructive
and can be used in series with other detectors. The TCD is a universal detector that is
concentration sensitive. The TCD sensitivity depends on the filament current, component
concentrations, and the difference in thermal conductivity between the carrier gas and the
component.
CAUTION
To prevent TCD filament damage, shut off the filament current

before disconnecting columns or turning off gas flows.
To set up a TCD, read the TCD setup summary, then follow the steps.
TCD Setup Summary

To set up a TCD:
1
Turn on the oven and detector heaters.
Equalize the makeup and reference gas flows.
Enter the TCD bridge current.
Balance the bridge.
1.
Turn on the Oven and Detector Heaters
1. Close the oven door.

This turns on the oven heater.
2. Press [Detect Control] [Detect Control].
TCD 2 NOT RDY
Temperature
102
35
Off
3. Type a TCD temperature appropriate for the analysis to be run, for example, 250 C.
TCD 2 NOT RDY
Temperature
45
250
4. Press [Enter].
Wait for the detector temperature to stabilize; as "NOT RDY" will disappear from the
above screen.
2.
Equalize the Makeup and Reference Gas Flows
The following procedures describe how to adjust the makeup and reference gas in the
Clarus GC.
CAUTION
The TCD flow module for reference gas is calibrated with helium
gas at the factory. You must recalibrate the TCD flow module if
you are using a reference gas other than helium.
For optimum performance, apply a minimum flow of 5 mL/min to each of the two
detector channels.
Adjust the Reference Gas

To adjust the reference gas use the regulator mounted on the pneumatics control panel.
1. Open the detector cover to expose the reference and analytical gas outlets and the
balance potentiometer.
103
Balance
Potentiometer
Reference Outlet
Analytical Outlet
Figure 22. Top view of a TCD.

2. Attach the tubing from the flowmeter to the end of the TCD analytical outlet.
3. Display the stopwatch screen by pressing [System] [System] [Enter].
4. Measure the column flow rate through the analytical channel.
5. Disconnect the flowmeter from the analytical outlet and connect it to the reference
outlet.
6. Measure the flow through the reference channel.
7. Repeatedly adjust (using the TCD reference flow knob) and measure the flow
through the reference channel until it is within 20% of the flow through the
analytical channel. Turn the knob clockwise to decrease the flow, counterclockwise
to increase the flow.
104
Reference
Flow Knob
TCD Ref Flow
Figure 23 Reference flow knob for a manual pneumatics TCD.

8. Remove the flowmeter.
3.
Enter the TCD Bridge Current Range
1. Select a bridge current range using the criteria in the following table.
CAUTION
Operating at too high a temperature can have an adverse effect on

filament life.
105
Bridge Current Range vs. Max. Detector Operating Temperature Table
Bridge Current Range

He or H2
4
3
2
1
Up to 100 C
Up to 300 C
Up to 350 C
Up to 350 C
Recommended Operating
Temperatures for the Following
Detectors
N2
Argon
Do not Use 4
Do not Use 3
Up to 110C
Up to 350 C
Do not Use 4
Do not Use 3
Do not Use 2
Up to 350 C
The correlation between bridge current and range is in following table:

Correlation Between Bridge Current and Range Table
Bridge Current (mA)

Off
40
80
120
160
Range Entry
0
1
2
3
4
2. Press [Range] [Range]. The following screen appears:

TCD 2
Range
Initial 0
3. Type the appropriate range, then press [Enter].
Note:
Entering a negative number reverses the detector polarity. For examples of reversing the
polarity, see Chapter 8, Practical Hints in the Clarus 400/480 GC Hardware Guide.
Balance the Bridge
1. Press [AutoZero] [AutoZero]. The Autozero screen appears and displays the value of
the background signal.
TCD 2 A/Z
Initial
106
334.5 mV
On
2. Allow the system to stabilize for about 20 min, then open the detector cover.
3. Locate the TCD Balancing Potentiometer (see Figure 8-14). Adjust the
potentiometer until the Autozero display reads between 0.0 and 20.0 mV.
4. Wait for drifting to stop as indicated by a constant reading on the display.
5. Reset the potentiometer to produce a reading between 0.0 and 20.0 mV.
Using a TCD with the Autosampler or GSV

When using a TCD with the autosampler or a GSV (Gas Sampling Valve) at high
sensitivity, a minor baseline upset may occur at the time of injection.
If the signal goes below zero, create an Autozero timed event to bring the signal back
before peaks of interest elute. Initiate a test run to determine the timed event setting.
107
Setting Up a NPD
To avoid injury, Do Not turn on the hydrogen gas unless a column is
connected to the NPD and all fitting connections have been leak
tested.
WARNING
WARNING
Nitrogen Phosphorus Detectors (NPD) use hydrogen gas. Before you

turn on the hydrogen gas to the NPD, ensure that a column is
connected to the NPD fitting inside the oven. Turning on the hydrogen
gas without first connecting a column to the NPD could create the
possibility of an explosion in the oven.
Turn off the hydrogen gas before disconnecting a column from the
NPD.
When two NPDs are installed, but only one NPD has a column
connected to it, plug the inlet of the NPD without a column with a
1/8-inch stainless steel plug (P/N N930-0061) to prevent hydrogen
from back-diffusing into the oven.
Since in manual pneumatics, the hydrogen pressure regulator and the
air needle valve have been turned off prior to shipment, first set the
hydrogen and air inlet pressures to 30 psig. Then measure and set the
gas flows as described in this chapter.
CAUTION
108
NPD Overview
The nitrogen phosphorus detector (NPD) is a highly specific thermionic detector for
organically bound nitrogen and phosphorus.
CAUTION
When using capillary columns with the NPD, Hydrogen is NOT a

recommended carrier gas. The additive effect of the hydrogen
carrier gas and the hydrogen detector gas affects the sensitivity
and selectivity because it produces an overall higher hydrogen gas
flow. If you are temperature programming, column flow changes
may produce a negative baseline drift.
The detector operates by electrically heating a glass bead, that contains an alkali metal, to the
point where it emits electrons. A mixture of hydrogen gas and air flows around the bead to
produce a hydrogen plasma. Stable intermediates are formed in the hydrogen plasma which
then capture the electrons emitted from the bead to produce ions. A polarizing field directs
these ions to the collector electrode, thereby creating a current which is amplified. Sensitivity
is affected primarily by the air flow, and selectivity is affected primarily by the hydrogen
flow.
A cross-sectional view of a NPD is shown in the following figure.
CAUTION
Chlorinated solvents MUST NOT be used with this detector. The

life and performance of the alkali bead will be severely impaired by
contact with chlorinated compounds. In general, any halogenated
compounds will degrade bead performance; therefore, avoid using
stationary phases containing these compounds whenever possible.
The use of solvents such as water, methanol or ethanol will also
reduce bead performance and life. Although these solvents may
still be used, they should be avoided whenever possible.
109
To The
Amplifier
Bead Transformer
Assembly
Collector
Bead
Flame
Jet
Air
In
Hydrogen
In
Column
Connector
Figure 24 Nitrogen Phosphorus Detector (NPD).
110
Setting Up a Manual Pneumatics NPD

To set up the manual pneumatics of the NPD, follow the steps outlined in the NPD Setup
Summary, then condition the NPD bead.
The plasma gas flow is controlled by a needle valve and on/off regulator on the pneumatics
control panel. The needle valve controls the amount of air and the on/off regulator controls
the hydrogen flow.
CAUTION
Do not overtighten the inner flow adjustment screw in the needle

valve or the on/off regulator. Overtightening damages the
mechanical device.
AIR
Figure 25 Gas Control Valves for the manual pneumatics NPD.

Each pneumatic control consists of an outer knob (which is used to turn the hydrogen or air
completely on or off), a cap, and an inner gas flow adjustment screw.
111
Removing the cap exposes the adjustment screw, which is used to control the gas flow. To
set the air, use a small thin screwdriver to turn the needle valve adjusting screw
counterclockwise to increase the flow and clockwise to decrease the flow. To set the
hydrogen, use a hex wrench to turn the adjustment screw clockwise to increase the flow and
counterclockwise to decrease the flow. The on/off regulator has an internal restrictor to allow
low flows (3 mL/min or less) with an inlet of 30 psig. Turn the on/off regulator knob
clockwise to increase the flow and counterclockwise to decrease the flow.
NPD Setup Summary

To set up an NPD:
1 Disconnect the hydrogen and air lines at the NPD bulkhead.
2 Adjust the hydrogen flow.
3 Adjust the air flow.
4 Reconnect the hydrogen and air lines.
1.
Disconnect the Hydrogen and Air Lines at the NPD Bulkhead
1. Open the detector cover.
Detector Cover
Figure 26 Location of the detector cover.
112
This exposes the NPD bulkhead fittings shown in the following figure.
Red Sticker
Bulkhead Fittings
Hydrogen Line
Air Line
Figure 27 The NPD bulkhead fittings.

Note:
The hydrogen line is marked with a red sticker. The air line is unmarked.
2. Disconnect the hydrogen line by loosening the nut that connects the
hydrogen line to the bulkhead fitting with a 7/16-inch wrench.
2.
Note:
Adjust the Hydrogen Flow
For safety reasons, the hydrogen pressure regulator is set in the off position (turned
completely clockwise) before it is shipped from the factory.
1. Turn on the hydrogen gas at the tank and adjust the line pressure to 30 psig.
2. Connect the tubing from a flow meter to the end of the
hydrogen line at the NPD. It is marked with a red sticker.
3. Turn the hydrogen pressure regulator outer knob fully counterclockwise to open it.
113
CAUTION
4. To expose the adjustment screw, remove the protective cap from the hydrogen pressure
regulator.
5. Insert the hex wrench in the adjustment screw and turn it clockwise to increase the flow.
6. Display the Stopwatch screen on the Clarus GC by pressing [System] [System] [Enter].
Stopwatch
0.00 min
Flow
Vol 1
7. Measure the flow rate. See "Using the Built-in Stopwatch" in Chapter 9, System
Utilities.
For best accuracy, use a soap bubble flowmeter volume that gives a reading of at least 30
seconds.
8. Continue adjusting the hydrogen flow until you obtain a flow rate of between 1.5 and 2
mL/min.
3.
Note:
Adjust the Air Flow
For safety reasons, the air needle valve is set in the off position (turned completely clockwise)
before it is shipped from the factory.
1
Turn on the air at the source and adjust the line pressure to 30 psig.
2. Connect the flowmeter to the end of the air line that is near the NPD.
3. Start the air flowing by turning the outer ring of the air control valve fully
counterclockwise (see Figure 25).
4. Remove the protective cap from the air control valve.
The stopwatch screen should still be displayed.
5. Measure the flow rate. For details, see "Using the Built-in Stopwatch" in Chapter 9,
System Utilities.
114
For best accuracy, use a soap bubble flowmeter volume that gives a reading of at least 30
seconds.
6. Adjust the air flow by turning the needle valve with the screwdriver.
Continue to measure and adjust the air flow until you obtain a flow rate of about 100 5
mL/min.
Reconnect the Air and Hydrogen Lines
1. Disconnect the flowmeter and reconnect the air line to the detector bulkhead.
Make sure the air line is connected to the unmarked bulkhead fitting.
2. Connect the hydrogen line (red sticker) to the detector bulkhead.
Make sure the hydrogen line is connected to the bulkhead fitting marked with a red
sticker.
CAUTION
CAUTION
When reconnecting the air and hydrogen lines to the bulkhead,

insert the tubing into the bulkhead fitting until it bottoms. Then pull
the tubing back slightly and tighten the nut to make a leak-free
connection. Do not overtighten the nut!
Any time the line pressure is changed from 30 psig, you must remeasure and adjust the air flows.
115
CAUTION
The flows listed in the above procedures for hydrogen and air are
optimum for both capillary and packed column flow rates. The
optimum flow provides the best sensitivity (signal to noise),
selectivity, and bead life. Any changes to these flows will affect all
of these parameters.
Also when using capillary columns, makeup gas is not required.
NPD Bead Activation Procedure

Packed Column Setup:
Disconnect column and cap the oven end of the detector. The recommended Detector
Cap Nut is in the 1/8-in. Plug Kit (P/N N9300061).
Capillary Column Setup:
With a capillary column connected, adjust Carrier flow to 0.5 mL/min or less (but not 0
), or (preferred) disconnect the column and cap the oven end of the detector.
Reactivating a Used NPD Bead
Preparing to Activate the NPD Bead

To activate a NPD bead:
NOTE: Never activate a NPD bead with a column connected to the detector fitting. To properly
activate the NPD bead, the column must be removed from the detector fitting and the detector
fitting must be capped.
1. Obtain a stopwatch or use the stopwatch function in the GC Utilities screen.
2. Open the oven door and allow the oven to cool.
3. Using a 7/16-inch wrench, loosen and remove the column nut from the detector
fitting. Remove the column from the detector fitting.
4. Install a 1/8-inch Swagelok plug (P/N N9300061) on the detector fitting. Provide a
leak-free seal by tightening the plug with a 7/16-inch wrench.
116
5. Close the oven door. Maintain a carrier gas flow through the column.
6. Install the bead in the conventional manner according to the installation procedure in
the GC Hardware Guide. Make sure that the bead does not contact any other surfaces.
7. Set the following conditions in the following order:
WARNING:
Set the Detector temperature to 150 deg. C. or greater. Wait for the detector
temperature to stabilize.
If a capillary column is used and is not disconnected from the detector, a high detector
temperature can cause bleed at the detector junction with the column. Make certain
the detector temperature is lower than the maximum temperature recommended for
the capillary column of your application.
-
Set the hydrogen and air flow as follows:
Air to 100 mL/min
Hydrogen to 2.0 mL/min
NOTE: Hydrogen flow accuracy is critical to proper NPD bead activation. Make certain that
the H2 flow is within 0.5 mL/min, or closer, to the H2 set point of 2.0 mL/min. Check
with a calibrated flow meter at the detector bulkhead that the flow is accurate if
activation problems occur.
NOTE:
Ensure that the hydrogen line is well purged of entrained air before you make the
final setting of hydrogen flow. Failure to purge the gas line from the hydrogen
supply (tank or generator) will result in an incorrect flow setting for operation and
can lead to poor operating performance and reduce bead life.
3. Set the detector range to x1.

4. From the system status screen touch the signal icon
background.
to display the detector
When the bead is off, the background value should be 0 0.25 mV. Write down the
background value that occurs with the bead off.
5. Open the detector cover (see Figure 4-26) and locate the bead potentiometer dial see (the
following figure).
117
If the NPD is detector 1 (front position), the potentiometer is located on the left side
of the panel. If the NPD is detector 2 (rear position) the potentiometer is located on
the right side of the panel.
Figure 4-28. Location of the Potentiometer Dial.

Activating the NPD Bead
The bead requires an activation step prior to use. Do not inject a sample during Activation.
To Activate the bead, carefully follow this procedure in sequential steps below:
1. Turn the bead potentiometer dial clockwise to apply current to the bead.
2. Slowly increase the NPD control voltage potentiometer to a setting of 700.
Note: The bead will gradually acquire an orange glow at this point.
3. Wait for 5 minutes then increase the potentiometer to 750.
4. After 1 minute move the potentiometer to 800.
118

7. After 1 minute reduce the potentiometer to 850.
10. After 1 minute reduce the potentiometer down to 700
11. For Capillary columns: Wait 10 minutes, go to the NPD detector screen, then
adjust the potentiometer so that the NPD baseline response reads around 0.5 mV on
Range 1. Then set the desired column flow for the application to be run.
For Packed Columns: Wait 10 minutes, go to the NPD detector screen, then adjust
the potentiometer down to 500 or below to drop the bead below the active level.
Remove the Detector Cap Nut (P/N N9300061) and reconnect the column to the
detector. Set the desired column flow for the application to be run, then again
increase the bead current potentiometer to give a reading around 0.5 mV on Range
1.
12. Allow the baseline to stabilize for 30 minutes.
13. Using the potentiometer, adjust the baseline between 0.4 and 0.6 mV at Range 1 and
the bead ready to use.
14. After conditioning the bead remove the Swagelok plug from the detector fitting and
reconnect the column.
15. Make sure the column flow is properly set. Touch the signal icon
to display
the detector background produced by carrier gas flow. The bead background will be
less due to cooling effects.
119
16. Turn the bead potentiometer dial clockwise until you achieve a reading of 0.25 mV
above the "off" reading with the detector range set to x1.
17. Once the system has stabilized, it is ready for operation.
If you are unable to achieve adequate sensitivity for your standard, increase the
background of the NPD. Increasing intervals of 0.25 mV are recommended.
Adjust the background setting to achieve the sensitivity required for your samples.
For example, if you have a concentrated sample, such as drugs, it can be analyzed
with a background of 0.25 0.50 mV. If you have a low-level sample, such as
pesticides, it may require a setting as high as 1 2 mV. To get the maximum life
from your NPD bead, operate at the lowest setting to achieve your required
sensitivity.
NOTE: (1) The bead will be stable after operating for several hours, but it will drift in time. At the
start of each day, adjust the background reading to the setting you are using and allow a few
minutes for it to stabilize.
(2) Due to the loss of alkali metal with use, the nature of the bead is to drift over time. We
strongly recommend using an internal standard for quantitative analysis.
(3) The bead can operate at higher background settings. The higher the setting, the greater the
signal and noise. Therefore, the signal to noise ratio will not increase dramatically. Operate at
the lowest possible setting to achieve the required sensitivity; this will also prolong the life of
the bead.
120
NOTE: The bead should be turned off by turning the bead potentiometer dial fully counterclockwise
before you turn off the Clarus GC. Remember that the bead has a finite life. You can extend
the bead life by turning the bead off when it is not in use for long periods of time (for
example, over the weekend).
Reactivate a Used NPD Bead

To increase the bead life, turn off the bead if the NPD is not continually in use. When you
turn off the bead, keep the detector temperature, hydrogen flow, and air flow set to operating
conditions. If the column remains connected to the injector and detector in the oven, make
sure the carrier gas is flowing through the column. If the column is disconnected from the
detector, make sure the Swagelok cap is installed on the NPD fitting.
Prior to using the NPD, adjust the bead background to the same millivolt setting that you
were using. Run your standards to determine if the NPD bead is responding at a level of
sensitivity equal to the previous run. If not, then reactivate the NPD bead.
To reactivate a NPD bead follow the activation procedure above.
Operating Notes
The bead is operated as a conventional NPD bead; following these instructions will increase
the bead lifetime.
Baseline: Set the baseline to a level of between 0.4 0.5. A lower baseline will help to
extend bead lifetime. Studies have shown that the signal-to-noise will not be adversely
affected by the lower baseline.
Column bleed: Material from the column can effect bead lifetime. Keep the maximum oven
temperature as low as possible for each application.
Between run operation: If the NPD bead is not in use for a few days it is best to simply
lower the potentiometer setting to 600 and maintain the detector temperature at 200 deg. C. or
greater. If the NPD detector will not be in use for an extended period, simply turn the
potentiometer to zero. To reuse the bead follow the activation procedure.
Loss in sensitivity the NPD bead is a consumable and will experience a loss in sensitivity
over time. Often, adequate sensitivity can be restored by repeating the activation process.
121
122
Controlling the
Clarus 400/480 GC
124
Clarus 400/480 Software Guide
Overview
The Clarus GC is controlled by a collection of operating parameters called the Active Method.
You can prepare and save up to five methods and make any one of them the Active Method.
However, Method 5 is typically reserved for external computer control of the Clarus GC. If you
are not controlling your Clarus GC from an external computer, you can use Method 5 in the
same way as you would use your other four methods.
Clarus GC operating parameters include such things as an oven temperature program; injector
temperature or detector temperature or a timed events table, and a variety of parameters for
controlling data output.
Active Method parameters are always saved when you turn the Clarus GC off, and
automatically reloaded when you turn it back on.
This chapter contains the following sections:
Viewing Active Method Parameters
Editing the Active Method
Method Utilities
125
Controlling the Clarus 400/480 GC
Viewing Active Method Parameters

The 12 parameter keys access the Active Method parameters when the system is not in the
Configuration Mode. To exit the Configuration Mode, press [Status Escape].
Function Keys
Method
System
Auto
BackGround
Run
Parameter Keys
Entry Keys
Oven
Temp
Time
Rate
Inject
Temp
Carrier
Gas
Valve
Detect
Temp
Range
Output
on yes
Atten
Auto
Zero
Events
off
Reset
Oven
Status
Escape
Delete
Enter
Set
CE
0 no
Control Keys
Figure 29 The parameter keys.

Note:
Only the Active Method can be edited directly from the parameter keys without going through
the Method menu. To view and edit a Stored method, see Editing a Stored Method. To
generate a new method, see Generating a Method.
The parameter keys are linked in sequence from left to right, top to bottom. To display the
first parameter screen, press [Oven Prog]. To display subsequent screens, press [Enter].
After selecting a parameter screen, the remaining parameter screens are arranged in a loop.
After displaying the last parameter screen, pressing [Enter] displays the first parameter
screen. You don't have to view the parameters in sequence. To view a specific parameter
screen, simply press the appropriate parameter key.
126
The following table lists the GC tasks and their corresponding parameter keys:
GC Task
Parameter Key
Setting up an oven temperature program
[Oven Prog], [Time], and [Rate].
Setting an injector temperature/program
[Inject Prog]
Setting a detector temperature
[Detect Control]
Viewing/setting carrier gas pressure/program
[Carrier Prog]
Viewing/setting carrier gas flow/program
[Carrier Prog]
Setting up valves
[Valve]
Setting FID, PID or NPD range
[Range]
Setting TCD filament current
[Range]
Routing detector output
[Output]
Attenuating detector signals
[Atten]
Autozeroing a detector
[AutoZero]
Building a timed events table
[Events]
Examples of method parameters are displayed on the next page.
127
Active Method Parameter Examples
The following sequence of method parameter screens was obtained by first pressing [Oven
Prog], then repeatedly pressing [Enter] to display subsequent screens.
Oven
TEMP 1
READY
75
75
Oven
READY
TIME 1
0.00m
999.9m
Oven
READY
RATE 1
75
End
Cap 1
READY
Pkd 2
READY
Temperature
Temperature
128
TEMP 1 is the initial oven temperature of an

oven temperature program.
125
125
150
150
TIME 1 is the Hold TIME for TEMP 1.
RATE 1 is the rate of temperature increase

(in C/min) to go from TEMP 1 to TEMP 2 in an
oven temperature program. "End" means a rate of
0C/min.
The top line displays the type of injector in position
1 (front) and its actual temperature. The bottom line
displays the setpoint.
The top line displays the type of injector in position

2 (rear) and its actual temperature. The bottom line
displays the setpoint.
Editing the Active Method

If you have read and used the chapters in this guide and the hardware guide, sequentially, as
recommended, by now you have probably installed and conditioned one or two columns, and
set up one or two detectors. Also, you were probably not aware at the time that you modified
certain Active Method parameters. Since the conditions used then were not necessarily those
required by the analyses you want to perform, you should now edit the Active Method to set
your operating parameters.
Examples of how to perform the tasks listed below are described in the sections which
follow. You should, of course, substitute your values for ours.
Setting up oven temperature programs
Setting detector temperatures
Setting up valves
Setting FID, PID or NPD range
Setting TCD filament current
Routing detector output
Attenuating detector signals
Autozeroing a detector
Building a timed events table
Up to this point, you have read Chapters 1 through 8, just installed a column, set up the
carrier-gas pressure or flow, and set up your detector. If this is the case, all gases are turned
on at the gas source, and the Clarus GC is on. If you have just set up an FID, you should
have ignited the flame.
Following the last of the above tasks is a section called "Method Utilities." It shows you how
to generate, set up, copy, delete, edit, and print a method.
Getting Ready to Edit the Active Method
Depending on what has occurred before you got to this chapter, the oven door may or may
not be closed. To make it easier for you to follow the examples presented in this chapter:
1. Close the oven door.
A status screen appears that is similar to one of the following:
129
Method 1 NOT RDY

Ovn Det Inj
40
Method 1 READY
75
Both the NOT RDY and READY status screens display the current active method
number. In the above example, Method 1 is the Active Method.
2. If you press [Status Escape] a second time, the total analysis time is displayed.
Whether the system is ready or not, you can proceed to the next section.
Note:
When you change an Active Method parameter, the change goes into effect immediately. For
example, if the system is READY and you change an injector temperature setpoint, the status
screen displays NOT RDY until the new setpoint is reached.
Setting Up Oven and Inlet Temperature Programs

The Clarus GC software allows you to set up four-ramp programs (they are 0 [isothermal], 1,
2, or 3) using the [Oven Prog], [Time], [Rate], [Inject Prog], [Time], and [Rate] keys. The
following figure is a schematic of GC temperature program steps.
Figure 30 Typical temperature program steps.

Before you actually set up an oven temperature program, you should decide on the
Equilibration Time you need and change the default value (2 minutes) if necessary (see
below).
Configuring the Equilibration Time
When you change the oven temperature setpoint, the system heats or cools the oven to the
new setpoint, then equilibrates the column(s) for the specified Equilibration Time before the
instrument becomes READY.
130
Note:
A minimum Equilibration Time of 2 minutes is recommended for temperature programs.

Longer equilibration times are recommended for initial oven temperatures of < 50C. An
equilibration time of 0.0 minutes can be used for isothermal methods.
To display the Equilibration Screen:
?
Press [System] [Enter] [Time].

Oven
Equil Time
The Equilibration Time that appears is the

default value.
Config
2.0m
If the Equilibration Time is satisfactory, press [Status Escape]. Otherwise, type in a new
time, then press [Enter] [Status Escape].
Setting Up an Isothermal Program

Setting up an isothermal program requires entering the following information in the sequence
shown:
Initial oven temperature (TEMP 1)
The total run time for the initial temperature (TIME 1)
A temperature rate increase of 0 (RATE 1).
To set up an isothermal program:

1. Press [Oven Prog].
Oven
TEMP 1
75
75
2. Enter a setpoint appropriate for your analysis, for example, 100 C.

Oven NOT RDY
TEMP 1
80
100
The oven status changes to NOT RDY. The

changing oven temperature is displayed on the top
line as the oven heats up to the new setpoint. When
the oven reaches the new setpoint, the system
equilibrates for the time specified in configuration
and then becomes READY.
131
For an isothermal run, TIME 1 is equivalent to the total run time. At the end of the time
(TIME 1), the system changes to NOT RDY, it equilibrates, and then goes READY.
To change the hold time:
3. Press [Enter].
Oven
TIME 1
0.00m
999.9m
The TIME 1 screen appears.
4. Enter a hold time appropriate for your analysis, for example, 25 min.
Oven
TIME 1
0.00m
25.0m
The display now shows the new total run

time.
5. Press [Enter].
Oven
RATE 1
Note:
100
End
The RATE 1 screen appears.
Since a constant oven temperature is maintained for isothermal operation, the rate of
temperature increase must be set to 0 . If the Active Method you are editing is already
isothermal, the RATE parameter will have been properly set at 0 and is indicated on the
screen by the word "End." If other than an isothermal program has been previously set up, a
value will appear on the screen. For example:
Oven
RATE 1
132
100
2 /m
To set the RATE to 0:

?
Press [0] [Enter] or press [Delete] [Enter]

The value is replaced with the word "End."
Note:
Whenever a RATE is set to 0, any subsequent program steps, if present, are deleted from
the Active Method.
Setting Up a One-Ramp Temperature Program
Setting up a one-ramp program requires entering the following information in the sequence
shown:
Initial oven temperature (TEMP 1)
Isothermal time for the initial temperature (TIME 1)
Rate of temperature increase from the initial to the final oven temperature (RATE 1)
Final oven temperature (TEMP 2)
Isothermal time for the final temperature (TIME 2)
Temperature increase of 0 C/min which signifies the end of the RATE 2 step.
The following example shows how to convert an isothermal program into a one-ramp
program using the previous isothermal method oven temperature parameter as a starting
point.
Parameter
Value
TEMP 1
50 C
TIME 1
5 min
RATE 1
2 C/min
TEMP 2
70 C
TIME 2
10 min
RATE 2
End (0 C/min)
To set up a one-ramp program:
133
1. Press [Oven Prog].

Oven
TEMP 1
NOT RDY
100
100
The TEMP 1 screen appears.
2. Enter 50 for TEMP 1.

Oven
TEMP 1
NOT RDY
90
50
The oven status changes to NOT RDY.

The changing oven temperature is
displayed on the top line as the oven cools
to the new setpoint.
3. Press [Enter].
Oven
TIME 1
NOT RDY
0.00m
25.0m
4. Enter 5 for TIME 1, then press [Enter].

Oven
RATE 1
NOT RDY
75
End
The RATE 1 screen appears.
5. Enter a ramp RATE 1 of 2 C/min, then press [Enter].

Oven
TEMP 2
NOT RDY
60
50
The TEMP 2 screen appears.
6. For TEMP 2, enter a temperature of 70 C, then press [Enter].

Oven
TIME 2
NOT RDY
0.00m
0.00m
The TIME 2 Screen appears.
7. Enter a time of 10 min, then press [Enter].

Oven
RATE 2
NOT RDY
51
End
The RATE 2 Screen appears.
8. If a value instead of End appears, press [0] [Enter] or [Delete] [Enter].
134
Setting Up a Multiramp Temperature Program

The example which follows shows how to expand the above one-ramp program to a tworamp program. The parameter values used in the example are shown below:
Parameter
Value
RATE 2
4 C/min
TEMP 3
100 C
TIME 3
5 min
RATE 3
0 C/min
If the RATE 2 screen is not on the display, press [Rate] twice to display it.
Oven
RATE 2
NOT RDY
60
End
1. Enter a rate of 4, then press [Enter].

Oven
TEMP 3
NOT RDY
60
70
The TEMP 3 Screen appears.
2. Enter a temperature of 100, then press [Enter].

Oven
TIME 3
0.00m
0.00m
The TIME 3 Screen appears.
3. Enter a time of 5, then press [Enter].

Oven
RATE 3
50
End
The RATE 3 Screen appears.
4. If "End" is not shown, press [0] [Enter] or [Delete] [Enter] to end the temperature
program.
Note:
You can enter RATE 3, TEMP 4, and TIME 4 to set up a third ramp.
135
Holding an Oven Temperature

While running a temperature program, you can hold the oven temperature by setting it to the
temperature of the unexecuted steps.
To hold an oven temperature during a temperature program:
1. Press [Reset Oven] and the following screen appears:
Reset to Oven Temp:
1
2
3
2. Press [->Set] to move the cursor from oven Temp 1 to Temp 2. Then press [Enter].
The oven heats ballistically to the temperature value for oven Temp 2 and holds, instead
of executing the time associated with oven Temp 2.
Figure 31 Oven Temperature Program for Rate 1.

3. Press the [Run] key to continue with the next program step or [Reset Oven] [Enter] to reset the
oven to the beginning of the temperature program.
To hold the oven program at a specific time during or before a run, use an oven HOLD
timed event. See the section on Timed Events.
Setting Injector Temperatures
The examples in this section were derived by editing the Active Method with a capillary
injector installed and configured in position 1 (front), and a packed injector installed and
configured in position 2 (rear).
This section contains examples of how to:
136
Display injector temperature screens
Change injector temperatures
Turn injector heaters off
Turn injector heaters on
Set oven programming mode
Set inlet programming mode
Displaying Injector Temperature Screens

1. Press [Inject Prog].
An injector screen similar to the following appears.
Cap 1
Temperature
150
150
2. To display the injector 2 screen, press [Enter], or press [Inject Prog] again.
Changing Injector Temperatures

1. Display the appropriate injector screen.
2. Enter an injector temperature setpoint of 275. The screen changes to:
Cap 1
NOT RDY
Temperature
165
275
The status changes to NOT READY until the injector heats up to the new temperature.
The screen then appears as shown below:
Cap 1
Temperature
275
275
Turning Injector Heaters Off

1. Display the appropriate injector screen, for example:
Pkd 2
Temperature
325
325
2. Press [Off/No 0]. The screen changes to:

Pkd 2
Temperature
325
0
137
3. Press [Enter]. The screen changes to:

Pkd 2
Temperature
295
Off
As the injector cools off, the injector temperature is displayed on the top line of the above
screen.
Turning Injector Heaters On

1. Display the appropriate injector screen, for example:
Pkd 2
Temperature
30
Off
1. Type in an appropriate temperature, then press [Enter].

Note:
Procedures for de-configuring or configuring injectors are described in Chapter 9, System

Utilities.
Viewing or Adjusting Carrier Gas Pressure

To view the display:
1. Press [Carrier Prog].
A display similar to the following appears for injector 1.
Pres 1
Set
25.4
25.0 psi
The screen displays a digital pressure readout of the actual pressure (top line) and the set
pressure (bottom line).
Note:
The Pressure Readout display units are configured by PerkinElmer as psi. If you want to
change the units to kPa, refer to Chapter 9, System Utilities.
2. If your Clarus GC has a second capillary injector, you can view its pressure screen by
pressing [Enter] from the first pressure display or [Carrier Prog] twice if another
parameter is on the screen.
To adjust the carrier gas pressure:
1. Type in a new setpoint value, for example, 20, then press [Enter].
The screen changes to:
138
Pres 1
Set
Note:
NOT RDY
25.4
20.0 psi
When the setpoint is greater than zero, the Clarus GC compares the setpoint and actual
pressure reading. If the actual pressure is not within the READY window, the "NOT RDY"
status appears. When the inlet pressure is within the READY window, NOT RDY disappears
from the screen.
SPLIT FLOW
Pressure
Control
Knob
CARRIER PRESSURE
Figure 32. Pressure control knob.

Note:
Entering a setpoint of 0 disables READY/NOT READY checking.
Setting the Septum Purge Mode and Offset

To set the septum purge offset:
1. Press [System] Config [Enter].
2. Repeatedly press [Enter] until the following screen appears.
Septum Purge 1
Auto
Fixed
Auto is the default and recommended for split operation, especially at split vent flows of
50 mL/min or less.
3. Press [->Set] to select the Fixed septum purge mode.
4. Enter the offset in mL/min:
139
Septum Purge 1
Flow
3.0 mL/min
Setting Up Valves
The Clarus GC operates six internal solenoid valves. Procedures for setting up Valves 1 or 2
for Split/Splitless operation controlled by manual pneumatics are provided in Chapter 5,
"Installing a Capillary Column" In the Clarus 400/480 GC Hardware Guide.
There are up to six valve screens, one for each configured valve. The specific valve screen is
displayed by pressing [Valve] one to six times. Alternately, you can display the screen for
Valve 1, then repeatedly press [Enter], to view subsequent screens.
An example of a valve screen configured capillary injector (CAP) is shown below:
Split 1
Initial
Note:
OFF
OFF
To immediately turn a valve on or off, press the [->Set] key.
Setting Detector Temperatures
The examples shown below assume that the Clarus GC is READY, an FID has been installed
and configured in position 1 (front), a TCD has been installed and configured in position 2
(rear).
This section contains examples of how to:
Display detector temperature screens
Change detector heater temperatures
Turn detector heaters off
Turn detector heaters on
Displaying Detector Temperature Screens

To display detector temperature screens:
1. Press [Detect Control] (detector temperature).
A screen similar to the following appears.
140
FID 1
Temperature
150
150
2. To display the detector 2 screen, press [Enter] or press [Detect Control] again.
Changing Detector Temperatures

To change a detector temperature:
1. Display the appropriate detector screen.
2. Enter a detector temperature setpoint of 275.
FID 1
NOT RDY
Temperature
165
275
The status changes to NOT RDY until the detector heats up to the new temperature. The
screen then appears as shown below:
FID 1
Temperature
275
275
Turning Detector Heaters Off

To turn a detector heater off:
1. Display the appropriate detector screen, for example:
TCD 2
Temperature
325
325
2. Press [Off/No 0].

TCD 2
Temperature
325
3. Press [Enter].
141
TCD 2
Temperature
295
Off
As the detector cools off, the detector temperature is displayed on the top line of
the above screen.
Turning Detector Heaters On
1. Display the appropriate detector screen, for example:
TCD 2
Temperature
Off
30
2. Type in an appropriate temperature, then press [Enter].

Note:
Procedures for deconfiguring or configuring detectors are described in Chapter 9, System

Utilities.
Setting the Range

Setting the FID or NPD Range
The initial FID or NPD range is set from the FID or NPD Range screen.
To view the FID Range screen:
? Press [Range].
The Range screen for the detector configured as detector 1 appears:
FID 1 Range
Initial
20
20
FID and NPD range options are 1 or 20, where 1 is the most sensitive setting and 20 is 20
times less sensitive.
To change the initial setting to 1:
? Press [1] [Enter].

142
FID 1 Range
Initial
The value that you enter will always be used unless you change it with a timed event.
For certain analyses such as those for trace or concentrated components, you may wish to
change the Range during a GC run. You can do this with a Timed Event. The following
example illustrates this.
Changing the FID or NPD Range During a Run

To automatically change the range from 1 to 20 after 2 minutes into the run:
1. Press [Events].
The following appears:
TIME
Event
Value
2. Enter a time of 2 min by pressing [2] [Enter].

TIME
2.00
Event
Value
3. Press [Range].
TIME
2.00
Event
Range 1
Value
1
The range shown is the initial value in the Active Method for detector 1. If detector 2 is
required, press [Range] a second time.
4. Press [20] [Enter].
TIME
2.00
Event
Range 1
Value
20
143
When a run is started, the system uses the initial range of 1 for 2 minutes, then
switches to a range of 20 for the duration of the run. When the run is completed, the
system switches back to the initial value of 1.
5. Press [Status Escape] to leave the timed event screen.
Setting the TCD Range (Filament Current)

The initial TCD range is set from the TCD Range screen.
? Repeatedly press [Range] until the TCD Range Screen appears:
TCD 2
Initial
Range
TCD range options are 0 (Off), 1, 2, 3, 4 (maximum sensitivity) and 1,2, 3, or -4. A
negative value reverses the polarity.
The TCD range values corresponding to bridge current are shown below:
Table 9-1. Correlation Between Bridge Current and Range
Range Entry
Off
40
80
120
160
0
1
2
3
4
To change the setting, for example, to 2:

? Press [- ] [2] [Enter].
TCD 2 Range
Initial
2
2
The initial setting is the range that is used at all times unless the polarity is
changed with a timed event during a GC run.
144
Changing TCD Polarity During a Run

TCD Range timed events are restricted to changing TCD polarity. For example, if an initial
range is four, then an event can only be entered for +4or -4. Examples for using polarity
changes are given in Chapter 8, Practical Hints In the Clarus 400/480 CG Hardware
Guide.
To automatically change the range from 2 to 2 after 3 minutes into the run:
1. Press [Events].
TIME
Event
Value
2. Enter a time of three minutes by pressing [3] [Enter]:

TIME
3.00
Event
Value
3. Press [Range] once or twice until the screen changes to:

TIME
3.00
Event
Range 2
Value
2
The Range value shown is the initial value in the Active Method.
TIME
3.00
Event
Range 2
Value
2
When a run is started, the system uses the initial range of 2 for 3 minutes, then reverses the
polarity for the duration of the run. When the run is completed, the system switches back
to the initial value, in this case 2.
5. Press [Status Escape] to leave the timed event screen.
145
Routing Detector Output

The Clarus GC contains one analog data output channel for each installed detector amplifier
board. You can attach an integrator or recorder to either output channel. In Chapter 4, you
configured each output channel for the device that you attached when you installed the
Clarus, for example, a 1-mV recorder or a 1-V integrator.
Normally the detector output would go to the device configured for that channel. However, if you
are running complex analyses, such as those requiring detector switching, you may wish to route
the signal to either channel.
Rerouting Output
Assume that:
Detector 1 is an FID whose output is going to an integrator

Detector 2 is a TCD whose output is going to a recorder
To immediately reroute the TCD 2 output to the integrator:

1. Press [Output].
The channel 1 output screen appears:
Int 1
Output
FID 1
Initial
FID 1
The top line displays whether an integrator or recorder is configured for the detector 1
output and which detector is connected to the device.
Int 1
Output
Initial
TCD 2
TCD 2
The TCD output is now going to the integrator.

Note:
Detector routing remains in effect until changed. The [Output] key is inactive unless two
detector amplifiers are configured as live detectors, and neither is configured as "Output." If
two detectors are installed but only one configured, then the output of the configured detector
is sent to both output channels.
146
Rerouting Output Using a Timed Event

Assume that you have carried out the previous procedure, for example, the TCD output is
going to the integrator. Here is how you would set up a timed event to route the FID output
to the integrator after five minutes into the run.
To reroute the output using a timed event:
1. Press [Events].
TIME
Event
Value
2. Enter a time of five minutes by pressing [5] [Enter].

TIME
5.00
Event
Value
3. Press [Output].
TIME
5.00
Event
Output1
Value
TCD 2
The above shows that the TCD output is going to channel 1 (the integrator). Enter the
number of the detector whose output you want sent to the integrator.
4. Press [1].
TIME
Event
5.00 Output1
Value
FID 1
When the run starts, the TCD output goes to the integrator. After 5 minutes, the FID
output goes to the integrator. When the run is complete, the TCD output goes to the
integrator.
147
Figure 33 Detector signal routing.

Attenuating Detector Signals Going to a Recorder
The purpose of attenuation when a recorder is attached and configured is to bring a peak on
scale by amplifying a weak signal or reducing an overly strong signal. Attenuation in this
case affects only the presentation of the signal.
Acceptable attenuation values are of the 2nd power, for example, 1, 2, 4, 8, 16, etc., up to a
maximum of 65,536. The system rounds off values to the next highest power of 2. For
example, if you enter 17 then press [Enter], an attenuation of 32 appears on the screen.
The range of attenuation values that may be used is 1 65,536. Raising the attenuation
decreases the signal to the recorder. Lowering the attenuation amplifies the signal to the
recorder.
To change an attenuation value:
1. Press [Atten] until the recorder screen appears.
Rec 2 Atten
Initial
2048
2048
2048 is the default value.
2. Type the new value, then press [Enter].

Recorder attenuation may be changed with a timed event.
A table listing attenuation vs. the maximum detector signal producing 100% deflection on a 1
mV-recorder is provided in Chapter 8, Practical Hints In the Clarus 400/480 GC
Hardware Guide.
148
Optimizing a Detector Signal to an Integrator for Maximum Sample

Dynamic Range
The Clarus GC contains improved electronics which significantly reduce amplifier noise.
This allows you to amplify the detector signal without getting a large increase in the noise
level. Therefore, it provides excellent minimal detection (signal to noise) for all Clarus GC
detectors. Amplification is set by pressing [Atten], the attenuation key, and entering an
attenuation value from x1 (most signal) to x64 (least signal). The maximum signal produced
by the Clarus GC amplifier is 1 V. To achieve the best sensitivity and widest dynamic range,
the sample with the highest concentration must not exceed the 1-V signal.
When using a flame ionization detector (FID), if you operate at range x1 and attenuation x64,
and the signal saturates (exceeds 1 V), then use range x20 and determine the appropriate
attenuation value (from x64 to x1) that produces a reasonable size peak. When using a
nitrogen phosphorus detector (NPD), the same will apply. When using an electron capture
detector (ECD), the only range setting is x1. To ensure that the signal does not exceed 1 V,
you should run your most concentrated sample at attenuation x64, then change the attenuation
to produce a reasonable size peak. When using a thermal conductivity detector (TCD) the
range or current setting also affects the output signal. Therefore, start at attenuation x64. As
long as the signal does not exceed 1 V, you can amplify the signal by changing the
attenuation.
Matching Detector Signals with Your Integrator

The following procedure should be followed if you are operating your detector near the
minimal detectable quantity level. This will ensure that the integrator is not filtering the
signal coming from the Clarus GC. The purpose of attenuation when an integrator is attached
and configured is to assure that the GC output is above the noise level of the integrator.
Normally, attenuation for an integrator need only be performed once. To obtain the most
satisfactory results, it is recommended that attenuation be carried out under actual operating
conditions prior to running your first sample.
Valid attenuation values when an integrator is configured are 1, 2, 4, 8, 16, 32, and 64.
The greater the attenuation, the smaller the degree of detector signal amplification.
Attenuation of an integrator can be thought of as a two-step process:
1. Observe the integrator noise at an attenuation of 64:
149
Figure 34 An example of integrator noise.

2. Gradually decrease the attenuation (for example, to 16 or until the noise level increases):
Figure 35 An example of detector noise.

A table listing attenuation vs. the maximum detector signal producing a 1-V output to an
integrator is provided in Chapter 8, Practical Hints In the Clarus 400/480 GC Hardware
Guide.
To change an attenuation value:
1. Press [Atten] until the Integrator Attenuation screen appears:
Int 1 Atten
Initial
2. Enter the new value, then press [Enter].

Note:
Attenuation of detector signals may be changed during a GC run with a timed event. At the
end of the GC run, the initial attenuation value is automatically restored.
150
Autozeroing a Detector
Each configured detector is equipped with digital autozeroing capability. As long as
Autozero is On, the system will autozero the detector to the offset specified during
configuration (see Chapter 3, Initial Setup Procedures) whenever the system becomes
READY or when a run is started. You can turn Autozero On or Off from the Autozero
screen.
To view the Autozero screen:
?
Press [AutoZero].

FID 1 A/Z
Autozero
1.09 mV
On
The actual value of the detector signal is displayed on the top line.
To manually autozero the detector:
?
Press [->Set].
The screen displays "Zeroed" for two seconds.

The output signal is set to the configured offset value for the selected output channel to
which the detector signal is routed (see Chapter 3, Initial Setup Procedures).
To turn off autozeroing for this detector:
?
Press [Off/No 0] [Enter].
Autozeroing can be set or turned off during a GC run with a timed event.
Note:
When Autozero is Off, the output signal is never autozeroed.
Building a Timed Events Table

The [Events] parameter key controls the timed events table. Events may be added, deleted,
and edited. Up to 32 timed events may be placed in the table.
Each event consists of three entries: the time at which the event is to occur, the name of the
event, and a value for that event. The [Events] key must be pressed for each new event to be
added to the table.
151
The events that may be included and the parameter keys that must be pressed to insert the
name of that event and its current value into the table are listed below:
Split vent flow with a capillary injector (CAP)
Turning valves 1 through 6 On or Off [Valve]
Changing the routing of the detector output [Output]
Changing FID or TCD range [Range]
Turning Autozero On or Off [AutoZero]
Attenuating the detector signal [Atten]
Holding the oven temperature program [Oven Prog]
Changing the carrier gas settings [Carrier Prog]
Entering a Timed Event

The example in this section assumes that a FID is in position 1 and that its output is going to
an integrator. Each line of the timed events table contains three fields: Time, Event, and
Value.
Events with negative times occur in ascending order after the equilibration time and before
the Clarus GC becomes ready. An event at 0.0 min occurs immediately upon starting a run.
Events with positive times occur in ascending order after the run starts.
The following procedure for completing a timed event line assumes that you are starting out
with a blank timed events table.
To enter a timed event:
1. Press [Events].
A blank line appears:
Time
Event
Value
2. Enter the time into the run that you want the event to occur, for example, 1.00 min, then
press [Enter].
The cursor moves to the Event field:
152
Time
1.00
Note:
Event
Value
Permissible time entries are from 99.00 to 999.00 minutes. Events may be entered that are
0.01 minutes apart.
3. Press an appropriate parameter key, for example, [Range]:
Time
1.00
Event
Range 1
Value
20
Press [Range] a second time to select a second detector's setting.

The name of the parameter and its current value are displayed. In the above case, Range
1 refers to the FID in position 1 and 20 is the current range value. The cursor moves to
the Value field.
4. To change the value, type a new value, then press [Enter].
153
Adding a Second Timed Event

1. To enter a new event, press [Events].
A new blank line appears.
Time
Event
Value
2. Enter a time of 2.00 min.

Time
2.00
Event
Value
3. Press an appropriate parameter key. For example, capillary injector (CAP), press
[Valve].
Time
2.00
Event
Split1
Value
ON
Adding a Third Timed Event

1. To enter a new event, press [Events].
A new blank line appears.
Time
Event
Value
2. Enter a time of 3.00 min.

Time
3.00
Event
Value
3. Press an appropriate parameter key, for example, [Atten].

154
Time
3.00
Event
Atten 1
Value
2048
Adding Additional Events

You can add additional events up to a maximum of 32 using the previous procedure.
Leaving the Timed Events Screen

?
Press [Status Escape]. A screen similar to the following appears:

Oven
TEMP 1
75
75
Displaying a Timed Events Table

If you could display the timed event parameters that you just entered in tabular form, it would
look like this:
Time
Event
1.00
2.00
3.00
Value
Range 1
Split1
Atten 1
20
On
2048
Scrolling Through the Timed Events Table

To scroll through the timed events table:
1. Press [Events].
A blank line appears:
Time
Event
Value
2. Press [Enter].
If timed events values exist, the first line of the table is displayed:
Time
1.00
Event
Range 1
Value
20
155
Press [Enter] repeatedly to display each successive line of the table.
Going Directly to a Line of the Timed Events Table

To go directly to a specific line in the timed events table:
1. Press [Events].
A blank line appears.
Time
Event
Value
2. Type the time of the event you want to display, for example, 3. The line for that time
appears:
Time
3.00
Event
Atten 1
Value
2048
Editing a Timed Events Table

To edit a timed events table:
1. Display the line you wish to edit.
2. Move the cursor to the field you want to change. For example, to change the time, type
the new time and press [Enter].
3. To change the event, press the appropriate parameter key.
4. To change the value, press the [Set] key to move the cursor to the value fields, then
type the new value, or press [On/Yes 1] or [Off/No 0], whichever is appropriate. Then
press [Enter].
Deleting a Timed Event

1. Display an event.
2. Press [Delete].
3. Press [Enter] to confirm or [CE] to cancel the delete.
156
Using a Timed Event to Hold the Oven Temperature Program
CAUTION
Use this feature only when you perform manual injection. If you use
the oven "Hold" feature with the autosampler, it will prevent the
Clarus GC from coming ready and therefore prevent it from
injecting!
Using a timed event to hold the oven temperature program will keep the GC in a "holding
pattern" until you press [Run].
Typically use this feature in conjunction with the splitter valve by setting the split valve
initially to OFF. This keeps the splitter valve closed (saving carrier gas) until the [Run] key
is pressed.
1.
Press [Valve].
The following screen displays:
Valve 1
Off
Initial
2. Press [Events].
A blank timed events screen appears:
Time
Event
Value
3. Enter a time of 1.00.

4. Press [Oven], then press [Enter].
Time
-1.00
Event
Hold
Value
5. Press [Events]. A new blank line appears.

6. Enter a time of 0.99.
7. Press [Valve]. The screen changes to:
Time
-0.99
Event
Valve 1
Value
157
8. Press [1] to set the value to On.

If you could display the timed event table, it would look like this:
Time
Event
1.00
Hold
0.99
Valve 1
Value
On
At one minute before the GC becomes "ready" (1.00), it will "Hold" at the current
settings until you press the [Run] key. Then at 0.99 min before "ready," the split vent
valve opens.
Note:
You must press the [RUN] key again, at the moment the injection is made, in order to start the
run.
158
Method Utilities
The software provides utilities for performing the following tasks:
Generating a new method
Setting up a stored method (making it active)
Copying a method
Deleting a method
Editing a stored method
Printing a method
Procedures for performing the above tasks are given in the subsections that follow.
To perform the above tasks you must first display the Method menu by pressing
[Method]. Page 1 of the Method menu appears:
Method 1
Setup Edit
Active
Copy >
Method Menu Page 1
Method 1
Gen Delete
Active
Print >
Method Menu Page 2
Generating a Method
The Gen option on page 2 of the Method menu allows you to generate a new method, using
default parameters as a starting point. To perform this task:
1. Display page 2 of the Method menu.
Method 1
Gen Delete
Active
Print >
2. Select Gen. The screen changes to:

Oven End: 999.0(Gen)
TEMP 1
75
159
Except for the top line, all parameter screens have the same appearance as those in the
Active Method. Procedures for viewing and editing parameters are identical to those
discussed above for the Active Method.
3. When you have completed entering the parameters, press [Status Escape].
The following menu appears:
Method
Save
Generated
Setup Discard
Saving the Generated Method

1. To save the generated method as a Stored Method, select Save. The following screen
appears:
Save
Note:
Gen
Method as #
4
5
The Active Method number does not appear.

You cannot save a Generated Method as the Active Method.
2. Select the number by which you want to identify this method, then press [Enter]. The
Status screen appears. If the method number you specified already exists, the following
appears:
Method # 2 Exists!
Cancel
Overwrite
If you select Cancel, the method will not be saved and the following appears:
Method
Save
Generated
Setup Discard
If you select Overwrite, the Status screen appears.
Setting Up the Generated Method

1. To immediately set up the generated method as the Active Method, select Setup from the
following menu:
160
Method
Save
Generated
Setup Discard

Setup Gen Method as
1
Cancel
The number that appears in the above menu is the method number that is active.
2. To complete the setup, press [Enter]. To cancel, select Cancel, then press [Enter].
Discarding the Generated Method

1. To delete the generated method, select Discard from the following menu:
Method
Save
Setup
Generated
Discard
2. Press [Enter].
Setting Up a Stored Method

To set up a method means to start using a Stored Method as the Active Method. To set up a
method, perform the following steps:
Method 1
Setup Edit
Active
Copy >
2. Select Setup. A menu displaying the numbers of all Stored Methods as well as the
Active Method appears:
Setup Method #
1
2
The cursor is positioned to the left of the method number that is active.
3. Select the number of the method to be set up, then press [Enter]. For example, if you
select 2 and then press [Enter], the System Status screen appears displaying the method
number that has been made active. For example,
161
Method 2 NOT RDY

Ovn
75
Method 2 is now the Active Method.
Copying a Method
Method 1
Setup Edit
Active
Copy >
2. Select Copy. The screen changes to:

Copy from Method #
1
2
4
5
This screen lists the numbers of all Stored Methods plus the Active Method number. The
cursor is positioned in front of the method number that is active.
3. Select the Method # to be copied, then press [Enter]. For example, if you select 5, the
following appears:
Copy Method # 5 to #
2
3
4
Since you cannot copy a Stored Method to the Active Method, its number does not
appear above.
4. Select the Method # to be replaced, then press [Enter].
Deleting a Stored Method

1. Display page 2 of the Method Menu.
Method 1
Gen Delete
Active
Print >
2. Select Delete.
A screen displaying the Stored Method numbers is seen. The Active Method and Stored
Methods specified in an autosampler program (see Chapter 7, "Controlling the
Autosampler") cannot be deleted. Their numbers are not displayed:
162
Delete Method #
2
3
4
3. Select the Method # to be deleted.

Delete Method # 3 ?
Cancel
Delete
4. Select an appropriate option, then press [Enter]. Page 1 of the Method menu appears.
Editing a Stored Method

When you edit a Stored Method, the changed parameters do not take effect until that method
is made active. To edit a Stored Method:
1. Display page 1 of the Method menu:
Method 1
Setup Edit
Active
Copy >
2. Select Edit, then press [Enter].

A menu similar to the following appears:
Edit Method #
2
4
5
The Active Method number does not appear. Only Stored Methods have their numbers
displayed. In the above example, the Active Method is Method #1. Method #3 has not
been stored.
3. Select the number of the Stored Method to be edited, for example 4, then press [Enter].
The parameters that now appear when you press a parameter key are those of the selected
Stored Method. The number of the method being edited appears on the right side of each
parameter screen. For example:
TCD 2
Temperature
(# 4)
200
4. After editing is complete, press [Status Escape].

163
Method # 4 Edited
Save
Abandon
5. Select the appropriate option, then press [Enter]. Abandon discards the edit and the
method is not changed.
Printing a Method
Note:
A printer must be attached and configured (see Configure a Printer in Chapter 4).
2. Select Print, then press [Enter].
Print Method #
1
2
3
4
3. Select the method # to be printed, then press [Enter].
164
Controlling the
Autosampler
166
Overview
Notes: 1. The autosampler will not respond to commands if the autosampler door is opened.
2. Only sample vials and syringes distributed by PerkinElmer should be used with the Clarus
GC.
3. Syringe plungers are not interchangeable from syringe to syringe.
The autosampler contains three basic parts: a syringe tower, a carousel, and a sample tray (see
following two figures). The syringe tower can contain either a 0.5-, 5.0-, or 50.0-L syringe.
The sample tray contains positions for eighty-two 2-mL sample vials. The turntable contains
one priority sample vial, four 4-mL waste vials, and four 4-mL wash vials.
Syringe Tower
Figure 36 Syringe tower.
167
Controlling the Autosampler
Autosampler Trays and Carousel

The Clarus 400 GC can use only the 82-vial standard tray or the 82-vial tall tray. The
Clarus 480 GC is designed to use the large capacity 108-vial tray for standard vials or the
108-vial tray for tall vials. There is also an 82-vial Thermostatting Tray Kit available for use
with the Clarus 400 GC and Clarus 480 GC.
The Standard vials are recommended and supplied by PerkinElmer. The Tall vials refer to
those vials not purchased from PerkinElmer which are slightly taller than the Standard vials.
Figure 37. 82-Vial sample tray and carousel.
168
82-Vial Standard Tray
Clarus GC
Model
Tray Capacity
of 2 mL Sample
Vials
108-Vial Standard Tray
Vial Height
Number of
4 mL Wash
Vials
108-Vial Tall Tray and Carousel

(for non-PerkinElmer vials)
Number of
4 mL Waste
Vials
Number of
2 mL Priority
Vials
480 only
108
Standard
480 only
108
Tall
400 only
82
Standard
400 only
82
Tall
With the Tray Thermostatting Accessory Kit

400/480
82
Standard
169
The autosampler can be configured to operate in one of two modes, Single- or MultiProgram.
Single-Program Mode In this mode, the autosampler runs a single autosampler

program that specifies which injector is to be used, the size of the injection, and the
number of injections per vial. Samples are injected sequentially starting with the first
occupied vial position. The GC is controlled by the parameters in the Active Method.
Multi-Program Mode In this mode, the autosampler runs two programs consecutively.
Each program specifies: the method to be used (each program can use a different method
if desired), which injector to use, the size of the injection, the number of injections per
vial, and the starting and ending vial numbers. As each program is run, the system sets
up the specified method as the Active Method. While running in this mode, the
autosampler attempts at least one injection from each vial in the specified ranges.
The remainder of this chapter includes the following procedures and topics:
Note:
Setting Up Syringe Wash Parameters
Setting Injection Mode Parameters
Running Samples in Single Program
Running Samples in Multi Program
Other Autosampler Tasks
The autosampler tray is keyed to fit correctly only in one direction. When installed properly,
the tray is recessed slightly around the entire Clarus GC top. If installed 180 out of position,
the tray will be angled (not lying flat) across the top of the instrument and will not allow the
tower to pass over it.
170
Syringe Wash Parameters

Syringe Wash parameters are common to both the Single- and Multi-program modes. In the
case of Multi-Program Mode, the parameters apply to both programs. It is suggested that you
set up these parameters prior to starting the autosampler. Enter the syringe wash parameters
on the Syringe Wash screen.
To display the syringe wash screen:
1. Press [Auto].
A/S
STOPPED
Prg Ctrl
START >
2. Select Ctrl, then press [Enter].
Edit Syringe Control

Washes
Mode
3. Select Washes, then press [Enter].
The Syringe Wash screen appears:
Pre Pump Post

2 6 2
Descriptions of the parameters on the Syringe Wash screen:
Pre the number of times the syringe is filled with sample and emptied to a waste vial
before a sample is acquired for injection. The default is 2. Permissible entries are 0 to
15. After entering a value, press [->Set].
Pump the number of times the syringe is repeatedly filled with sample before a
sample is acquired for injection (typically used to eliminate bubbles). The default is 6.
Permissible entries are 0 to 15. After entering a value, press [->Set].
Post the number of times the syringe is filled with solvent and emptied to waste after
sample injection. The first half of these washes is taken from solvent vial #1 or #3, the
second half from solvent vial #2 or #4. This operation is performed to clean the syringe
between samples. The Default is 2. Permissible entries are 0 to 15.
171
Injection Mode Parameters

Injection Mode parameters are common to both the Single- and Multi-Program Modes.
In the case of a Multi-Program Mode, the parameters apply to both programs. It is
suggested that you set up these parameters prior to starting the autosampler. Select the
Injection Mode on the Injection Mode screen.
To display the Injection Mode screen:
1. Press [Auto].
A/S
STOPPED
Prg Ctrl START >
Washes
Mode
3. Select Mode, then press [Enter].
The Injection Mode screen appears:
Edit Injector Mode
FastNormal Slow
Description of the settings the Injection Mode screen:
Fast the injection takes about 300 ms.
Note:
The "Fast" injection speed is not available when a 50.0-L syringe is installed.
Do not use the "Fast" mode with the 0.47-mm O.D. needle.
CAUTION
Normal the injection takes about 1 s.

Slow injection takes about 7.5 s. Select this option if you have installed a wide-bore
capillary column in the packed injector and are doing HOT on-column injections.
172
CAUTION
For on-column injection, the autosampler must be equipped with the 0.47mm O.D. needle.
173
Running Samples in Single-Program Mode

Before running samples in the single-program, make certain that:
A column and a syringe are installed.
The carrier gases and detectors are set up.
In the case of an FID that the flame has been ignited.
The zone temperatures have been specified in the Active Method.
The wash vials have been filled with solvent.
The sample vials have been placed in the sample tray.
The following steps summarize how to run samples in Single-Program Mode:

1. Configure for Single-Program Mode operation.
2. Enter Single-Program Mode parameters.
3. Set up a method.
4. Start the autosampler.
1.
Configure for Single-Program Mode

1. Press [System] [Enter] [Enter].
The Automation Configure screen appears:
Single Multi Off
2. Select Single, then press [Enter].
A/S Syringe Config
0.5L 5.0L 50.0L

3. Select the syringe size installed, then press [Enter].
Auto Program Config
Auto Resume Off
174
Recovering from a Power Failure

The previous screen provides the option for an autosampler program to automatically resume
where it left off should a power failure occur. In addition, you can select a specific method.
Auto Program
Auto Resume
Config
Off
1. Press [On/Yes 1], then press [Enter].

PowerUp Meth
Config
Auto 1 2 3 4 5
2. Select Auto or a specific method number, then press [Enter].
If you select Auto, then upon powerup, the Clarus GC will set up the method that
was running when the power was lost and run it once without injecting a sample. The
automation sequence that was interrupted is resumed.
If you select a specific method (1-5), then upon powerup, the Clarus GC will set up
that method and run it once without injecting a sample. The automation sequence
that was interrupted is resumed.
2.
Enter Single-Program Mode Parameters
1. Press [Auto].
Page 1 of the 2-page Autosampler Menu appears:
A/S STOPPED
Prg Ctrl START >
2. Press [Enter].
Injector L Inj/Vial
1.0 1
175
3. Enter the injector # to be used (for example, 1 for position 1 or 2 for position 2), then
press [->Set].
The cursor moves to L.
Injector L Inj/Vial
1 1.0 1
If a 0.5- L syringe has been configured, you may enter a volume from 0.0 to 0.5
L in steps of 0.1 L.
If a 5- L syringe has been configured, you may enter a volume from 0.0 to 5.0 L
in steps of 0.5 L.
If a 50- L syringe has been configured, you may enter a volume from 0.0 to 50.0
4. Enter the volume to be injected, then press [->Set].

Injector L Inj/Vial
1 1.0 1
The cursor moves to Inj/Vial.
5. Enter the # of injections per vial (1 through 15), then press [Status Escape].
176
3.
Set Up a Method
If you want to run the Clarus GC under the control of a method other than the current Active
Method, follow this procedure. Otherwise skip to step 4 (Start the Autosampler).
1. Press [Method] [Enter].
If the Active Method is Method # 1, a screen similar to the following appears:
Setup Method #
1 2 3 4 5
The above example assumes that you have created and saved five methods.
2. Select the desired method #, then press [Enter].
3. Press [Auto] to display the Autosampler Menu.
A/S
STOPPED
Prg Ctrl START >
4.
Start the Autosampler
With page 1 of the Autosampler Menu on the screen:

A/S
STOPPED
Prg Ctrl START >
Select START, then press [Enter]. The autosampler starts and a screen similar to
the following appears:
A/S
V01 Inj01
Prg Ctrl Paus STOP >
The top line displays the autosampler status, namely:
The vial number being injected (V01).
The injection number (Inj01).
177
Running Samples in Multi-Program Mode

Before running samples in the Multi-Program mode, make certain that:
A column and a syringe are installed.
The carrier gases and detectors are set up.
In the case of an FID, that the flame has been ignited.
The zone temperatures have been specified in the Active Method.
The wash vials have been filled with solvent.
The sample vials have been placed in the sample tray.
The following steps summarize how to run samples in Multi-Program Mode:

1. Configure for Multi-Program Mode operation.
2. Enter program 1 parameters.
3. Enter program 2 parameters.
4. Start the autosampler.
1.
Configure for Multi-Program Mode
1. Press [System] [Enter] [Enter].

Single Multi Off
2. Select Multi, then press [Enter].
A/S Syringe Config
0.5L 5.0L 50.0L
3. Select the syringe size installed, then press [Enter].
178
Auto Program
Auto Resume
Config
Off
Recovering from a Power Failure

The previous screen provides the option for an autosampler program to
automatically resume where it left off should a power failure occur.
Auto Program
Auto Resume
Config
Off
1. Press [On/Yes 1], then press [Enter].
2.
Enter Program 1 Parameters
1. Press [Auto].
Page 1 of the 2-page Autosampler menu appears:
A/S
Prg
STOPPED
Ctrl START >
2. Press [Enter].
Edit Program #
2
3. Press [Enter].
Prog Meth Start Stop
1 1 01 82 >
4. Type the # of the method to be used [for example, 0 (Off) through 5], then press [Enter]
[->Set].
Note:
To select a method in this screen, you must have previously saved the method.
179
Note:
Entering a method number of 0 (Off) disables the program.

The cursor moves to Start.
1 1 01 82 >
5. Type the starting Vial # (1 through 82), then press [Enter] [->Set].
You can enter vial numbers that wrap around. For example, you can start at vial 75 and
end at vial 21.
The cursor moves to Stop.
1 1 01 82 >
6. Type the last Vial # for program 1, then press [Enter] [->Set].
Prog Inj L Inj/Vial
1 1 1.0 1 >
7. Type the injector # to be used (injector 1 or 2), then press [->Set].
The cursor moves to L.
Prog Inj L Inj/Vial
1 1 1.0 1 >
If a 0.5- L syringe has been configured, you may enter a volume from 0.0 to
0.5 L in steps of 0.1 L.
If a 5- L syringe has been configured, you may enter a volume from 0.0 to 5.0
If a 50- L syringe has been configured, you may enter a volume from 0.0 to
50.0 L in steps of 5.0 L.
8. Type the volume to be injected, then press [Enter] [->Set].

The cursor moves to Inj/Vial.
180
Prog Inj L Inj/Vial

1 1 1.0 1 >
9. Type the # of injections per vial (for example, 1 - 15), then press [Status Escape]
[Status Escape].
A/S
STOPPED
Prg Ctrl START >
3.
Enter Program 2 Parameters

With the Autosampler menu on the screen:
1. Press [Enter].
Edit Program #
2
2. Select 2, then press [Enter].

2 Off 01 82 >
Enter parameters using the procedures in the previous section. A method of "Off" means
that the program will not be executed.
4.
Start the Autosampler
1. Press [Auto].
Page 1 of the 2-page Autosampler menu appears:
A/S
Prg
Ctrl
STOPPED
START >
2. Select START, then press [Enter].

The run starts and the following screen appears:
181
A/S
Prog1 V01 Inj01
Prg Ctrl Paus STOP>
The top line displays the autosampler status, namely:
182
The program # being run (Prog1).
The vial number being injected (V01).
The injection number (Inj01).
Other Autosampler Tasks

Autosampler tasks include the following:
Using solvent pre-washes.
Running viscous samples.
Cleaning the syringe.
Printing autosampler program(s) or the autosampler log.
Pausing and resuming an autosampler run.
Stopping or parking the autosampler.
Inserting a priority sample.
Procedures for performing these tasks are described below.
Using Solvent Pre-Washes

Pre-washes refers to the number of solvent washes you want the system to perform prior to
the pre-injection sample washes. Acceptable values are 0, 1 or 2. Pre-washes occur only at
the beginning of an autosampler program.
To specify the number of pre-washes desired:
1. Press [Auto].
A/S
STOPPED
Prg Ctrl Start >
Washes
Mode
Pre Pump Post
2 6 2 >
4. Display the second page of this menu.
Solv Visc
0 0
183
5. Select Solv, then press [Enter].

6. Type 0, 1, or 2 then press [Enter].
Running Viscous Samples

The Clarus GC allows you to vary the length of time the plunger pauses at the top-of-stroke
when acquiring samples. In addition, the plunger speed also slows down during injection.
The more viscous the sample, the higher you should set this value. To optimize
reproducibility you should experiment with different values.
The plunger speed during sample acquisition and injection will vary with the viscosity of the
sample. To find the optimum setting for the sample being analyzed, you should experiment
with various syringe settings.
To display the appropriate screen:
1. Press [Auto].
A/S
Prg
STOPPED
Ctrl Start >

Washes
Mode
Pre Pump Post
2 6 2 >
4. Display the second page of this menu.
Solv Visc
0
>
5. Select Visc.
6. Enter a value between 1 and 15. This value is the number of seconds the plunger
pauses at the top-of-stroke during sample acquisition.
Note:
You can obtain improved precision with viscous samples by using the 0.5-mL syringe and
septa in the waste/wash vials in place of the diffusion caps.
184
Cleaning the Syringe

1. To display page 2 of the Autosampler menu, press [Auto] [Auto].
A/S
STOPPED
Park Clean Print >
Note:
The Clean option is only available when the autosampler has stopped.
2. Select Clean, then press [Enter].
A/S Cleaning Syringe
Prg Ctrl STOP
The system performs the number of solvent washes specified in the Post parameter of the
Syringe Wash screen shown below:
Pre
2
Pump Post
6
2
In the above screen, the system will perform 2 solvent washes.
Cleaning the 5-L and 50-L Syringe Plungers

The 5-L and 50-L syringe plungers should be cleaned regularly, after approximately 500
injections, since insolubles can build up and cause friction.
185
To clean the syringe plunger:

1. Remove the syringe using the procedure in the preceding section.
2. Remove the plunger from the syringe barrel.
3. Wipe the plunger with a tissue soaked in an appropriate solvent.
4. Replace the plunger.
5. Pull and expel the same solvent through the barrel several times.
6. Replace the syringe using the procedure in the preceding section.
Note:
Only syringes distributed by PerkinElmer should be used with the Clarus GC. Plungers are
not interchangeable from syringe to syringe.
Printing
If a printer is connected and configured, you can print the contents of an autosampler
program or programs, or an Automation Log.
1. Select the Print option from page 2 of the Autosampler menu by pressing [Auto] [Auto].
A/S
STOPPED
Park Clean Print >
2. Select Print, then press [Enter].
Print Automation
Programs
Log
3. To print the autosampler programs, select Programs and then press [Enter].
4. To print the autosampler log, select Log and then press [Enter] to display the following
menu:
Print Automation Log
No Once Always
186
Select No to stop printing the Log after each autosampler program.
Select Once to print the current Log.
Select Always to automatically print the Log after all programs have been completed,
or upon stopping the autosampler.
PerkinElmer Clarus 400 GC

Automation Log
Method:
#/Vial:
Inlet:
uL
1.0
Vial #
Injections
1
2
3
0
Status
ok
No vial
Figure 38 Example of an Automation Log.
Pausing and Resuming an Autosampler Program

1. Press [Auto].
A/S Prog1 V01 Inj01
Prg Ctrl Paus STOP>
Paus suspends the autosampler program; an injection in process is first completed before
the program is suspended. While the autosampler is paused, you can edit an autosampler
program (select Prg), or change the Syringe Parameters (select Ctrl).
2. To pause an autosampler run, select Paus, then press [Enter].
A/S Prog1 V01 Inj01
Prg Ctrl Resm STOP>

Paus has been replaced by Resm (resume).
3. To resume a paused autosampler program, select Resm, then press [Enter].
Stopping the Autosampler

1. Press [Auto].
187
A/S Prog1 V01 Inj01

Prg Ctrl Paus STOP>
2. To stop the autosampler, select STOP.
The autosampler stops immediately and the syringe is withdrawn.
Parking the Autosampler Tower

Select the Park option at any time from page 2 of the Autosampler screen by pressing
[Auto] [Auto].
A/S
STOPPED
Park Clean Print >

The autosampler tower must be parked in order to change the syringe. Refer to the
Maintenance chapter in the Clarus 400/480 GC Hardware Guide, for instructions on
changing the syringe. If you select this option during an injection sequence, the autosampler
will move to the Park position after the current injection is made.
Note:
If the syringe is directly over an injector, you should move it by selecting Park from the above
menu.
Inserting a Priority Sample

This option instructs the autosampler to interrupt the vial injection sequence and inject a
"Priority" vial that has been placed in the "Priority" position of the turntable. The priority
vial will be injected after completion of the current run.
After the priority vial has been injected (in accordance with the current program parameters),
and the priority run completed, the program continues with the next injection in sequence.
Note:
Priority can only be selected when the Autosampler Program is active.

To inject a priority sample, while automation is running or paused:
1. Press [Auto] [Auto].
Page 2 of the Autosampler Status screen appears.
A/S Prog1 V01 Inj01
Park Prior Print >
188
2. Select Prior, then press [Enter].

Priority Injections
Remaining
0
3. Enter the number of priority injections (0 15). As the injections occur, the counter
decreases.
During the injection of a priority vial, the top line of the above status screen changes to:
A/S Prog1 Pri Inj01
Prg Ctrl Paus STOP>
... and the System Status screen contains PRI to indicate that a priority vial is being
injected. For example,
Method 1 PRI READY
75
189
About Waste and Wash Vials

The Autosampler software has been optimized to use waste vials and solvent wash vials to
minimize contamination of the syringe needle.
Septa are available for the waste vials and solvent wash vials by ordering P/N N930-2780.
We recommend using these septa in place of the diffuser caps when you are using:
Very viscous samples (to wipe the sample off the outside of the syringe needle).
Toxic solvents and samples.
Very volatile solvents.
Single-Program Mode
Waste Vials
When operating in the Single-Program Mode, the sample pre-washes are emptied into waste
vial #1 and #3 (alternating from one injection to the next). The solvent post-washes are
emptied into waste vial #2 and #4 (alternating from one injection to the next).
Wash Vials
When using solvent washes, injection 1 uses solvent from solvent wash vial #1, injection 2
uses solvent from wash vial #2, injection 3 uses solvent from wash vial #3, injection 4 uses
solvent from wash vial #4, injection 5 uses solvent from wash vial #1, etc.
Multi-Program Mode
Waste Vials
When operating in the Multi-Program Mode, the sample pre-washes are emptied into waste vial
#1 for program 1 and waste vial #3 for program 2. The solvent post-washes are emptied into
waste vial #2 for program 1 and #4 for program 2.
Wash Vials
Program 1 splits between solvent wash vials #1 and #2. For example, if four washes are
required, two will be taken from vial #1, and two will be taken from vial #2.
190
Program 2 splits between solvent wash vials #3 and #4. For example, if five washes are
required, three will be taken from vial #3, and two will be taken from vial #4.
About Sample Vials

Use 2-mL vials with the autosampler (P/N N9301385, 144 per box). These are crimp-top
vials. The vials and crimp caps with septa (P/N 00092205, 1000 per box) are available
through PerkinElmers catalog service (in the U.S., call: 1-800-762-4000).
The minimum volume of sample required in the 2-mL vial is 0.35 mL or 350 L. You should
fill the vial when running multiple injections per vial.
A mini-vial insert is available for laboratories with small sample volume requirements. This
insert fits into the standard 2-mL vial and requires a minimum volume of 5 L of sample.
These inserts are available through PerkinElmers catalog service.
Note:
1. When using mini-vials, it is not recommended to use pumps to acquire samples. This
assures that the sample will not be diluted by residual solvent in the syringe.
2. Only PerkinElmer vials should be used with the Clarus 400 GC.
3. Adjust the crimper so that it does not deform the vial cap and septum, but crimps the vial
cap tight enough so that you cannot turn the cap. An improperly adjusted crimper cam cause
the autosampler to malfunction.
191
Using a TCD with the Autosampler

When using a TCD at high sensitivity with a GSV or the autosampler, a minor baseline upset
may occur at the time of injection.
If the signal goes below zero, incorporate a timed event Autozero to bring the signal back to
zero before the peaks of interest elute.
Observe the initial chromatogram to determine the proper time for the timed event.
Available Syringes
The following syringes are available for the Clarus 400/480 GC:
Syringe
Part Number
5-L (0.63 mm O.D.) Teflon-tipped plunger (Std)
N6101390
0.5- L (0.63 mm O.D.)
N6101252
0.5- L (0.47 mm O.D.)
N6101253
5- L (0.63 mm O.D.)
N6101251
5- L (0.47 mm O.D.)
N6101380
50- L (0.63 mm O.D.)
N6101760
192
Background
Compensation
194
Overview
Background compensation is a routine that automatically subtracts a stored baseline profile
from the signal generated during a GC run.
Before background compensation can be applied to a detector output signal, the baseline
profile must be calibrated. The [Background] key controls both calibration and
compensation.
Calibration involves running a blank using your temperature program. Once run, the
background profile is stored. This profile is overwritten if calibration is rerun, thus only the
most recent profile is used for compensation.
One background profile is stored for each detector. Calibration and compensation can be
applied independently to each detector output signal.
Note:
The calibration run time must be greater than 2 minutes.
195
Background Compensation
Calibrating a Baseline Profile

Before starting a calibration run, make certain that:
Note:
All gas controls have been set.
The system is READY.
The column is well conditioned and clean.
The Active Method contains at least a one-step Oven Temperature program.
Calibration and Compensation will not work for an isothermal method.

To calibrate a baseline profile:
1. Press [Background].
Background 1 Off
On Calibrate
If a background profile has never been calibrated, the screen appears as follows:
Background 1
Calibrate
Off
2. Select Cal, then press [Enter]. The Background Calibration Menu for detector 1
appears.
Calibrate B/G 1
Off Once Multiple
To display the Calibration Menu for detector 2, press [Background] [Background].
Calibration Menu Options

Once The background profile will be calibrated once and stored. This profile is applied
automatically to all manual or autosampler runs when you subsequently turn the
background compensation On.
196
Multi The system runs the calibration method over and over again until you turn off
calibration in the Calibration Menu. You may wish to use this option, for example, to
condition a column overnight.
Note:
The system stores only the most recent calibrated background profile.
Off Select this option to turn calibration off.
3. Select "Once" or "Multiple," then press [Enter].
A screen similar to the following appears.
Background 1 Off
Off Calibrate
4. Then press [Status Escape].
When equilibration is complete, the System Status screen appears. For example,
B/G Cal
READY
75
5. Press [RUN].
The system runs the oven temperature program once or multiple times and stores the
baseline profile. In Multi, press [Run] to initiate the start of automatic cycling.
197
Background Compensation
Turning Background Compensation On

To apply background compensation to all subsequent manual or autosampler runs:
1. Display the appropriate Background menu. For example,
Background 1 Off
On
Calibrate
2. Press [Enter] to turn the background on.
Now every time a GC run is made, the calibrated and stored baseline profile will be
subtracted.
Turning Background Compensation Off

1. Display the appropriate Background menu. For example,
Background 1
On
Off
Calibrate
2. Press [Enter] to turn the background off.
198
System Utilities
Overview
The software contains utilities that enable you to:
Note:
Use the built-in stopwatch.
Configure the Clarus GC.
Calibrate the optional flow readout.
Print the run log.
Print the system configuration.
Lock and unlock the keyboard.
Calibrate the oven temperature.
Deconfigure and configure injectors.
Deconfigure and configure detectors.
your analysis.
You access these utilities from the System Control menu. To display the System Control
menu, press [System]. The first page of the two page System Control menu appears.
System Control
Confg
Lock >
System Control
Stpwtch Extrn
Prnt >
201
System Utilities
Using the Built-in Stopwatch

The software includes a stopwatch function that automatically calculates and displays the
carrier gas flow.
To use the stopwatch with a soap bubble flowmeter:
1. Press [System].
The first page of the System Control menu appears:
System Control
Confg Lock >
2. Press [System] again.
The second page of the System Control menu appears:
System Control
Stpwtch Extrn Prnt>
3. Press [Enter].
The Stopwatch screen appears:
Stopwatch
0.00 m
Flow
Vol 1
4. Enter the volume of the flowmeter you are using.

For example, change the default to 10 mL by typing [1] [0], then pressing [Enter]. The
screen changes to:
Stopwatch
0.00 m
Flow
Vol 10
Start the Stopwatch

5. When the bubble reaches the first graduation mark, press [Enter]. This starts the
stopwatch.
The elapsed time and calculated flow appear on the screen and are continuously updated.
For example,
202
Stopwatch
0.50 m
Flow 2.0
Vol 10
Stop the Stopwatch

6. When the bubble reaches the second graduation mark, press [Enter].
The system freezes, calculates, and displays the flow at that point. For example,
Stopwatch
2.50 m
Flow 4.0
Vol 10
Reset the Stopwatch

7. Press [CE].
Note:
The Stopwatch is a lap counter. As it runs, the time and flow are displayed on the screen. By
pressing [Enter], you can freeze this display without stopping the Stopwatch from counting.
This allows you to read the carrier gas flow for a specific point in time. When you press
[Enter] a second time, the display is updated to the current time and flow and continues to
reflect this information until you stop it again.
203
System Utilities
Configuring the Clarus GC

Your Clarus GC has been configured at the factory to correctly reflect the installed injectors
and detectors. However, there are operational requirements that you must configure before
using your Clarus GC.
Entering the Configuration Mode

1. Press [System].
The first page of the two page System Control screen appears. If you want to display
additional System Control selections as shown in the screen on the right, press [->Set]
three times.
System Control
Confg PPC Lock >
System Control
Stpwtch Extern >
2. If necessary, press [->Set] to move the cursor to the left of Confg (as shown above), then
press [Enter] to enter the Configuration mode.
If the autosampler is installed, the
If the autosampler is not installed,

the following screen appears:
None Autosamp
Oven Maximum Config

Temp Limit
450
Displaying Configuration Menus

Once in the Configuration Mode, you can scroll through the menus by repeatedly pressing
[Enter]. When viewing the last configuration menu, pressing [Enter] returns you to the
beginning of the configuration mode by redisplaying the first configuration menu. The total
number of configuration menus that appear depend on the hardware installed.
To familiarize yourself with the configuration menus, scroll through all of the menus by
repeatedly pressing [Enter]. Once familiar with the overall configuration of your Clarus GC,
you can go directly to most configuration menus by first entering the configuration mode (by
pressing [System] [Enter]), then pressing the appropriate key(s) as shown in the following
table:
204

Configuration Menus Table
First press [System] [Enter] then press

following key(s):
Oven Maximum Temp Limit

Setting
[Oven Prog]
[Oven Prog] [Enter]
[Time]
Sleep Time
[Time] [Time]
Heating Delay Configuration
[Time] [Time] [Time]
Time of Day Clock
Start Time

[Time]
Injector Type
[Inject Prog]
Detector Settings
[Detect Control]
[Output]
Output Offset
[Auto Zero]
Autosampler Mode
[Auto]
For additional configuration information, refer to Chapter 4, Initial Setup Procedures.
205
System Utilities
Calibrating the Flow Readout Using Manual

Pneumatics
It is only necessary to recalibrate the optional flow readout using manual pneumatics if you
have replaced the 0 to 100 mL/min flow element. If you are using a carrier gas other than
helium, you do not have to recalibrate. However, you must define the carrier gas on the
screen. If you do wish to recalibrate, use the procedure which follows.
The optional flow readout comes with a 0 to 100 mL/min flow element. If the optional flow
readout has been installed, it will have been calibrated at the factory using helium as the
carrier gas. Perform the following procedure if you have installed the 0 to 20 mL/min flow
element.
Note:
The flow controller is calibrated at 90 psig inlet.
CAUTION
At the moment the Clarus GC is turned on, the oven,

injector(s), and detector(s) begin to heat up rapidly. To
avoid injury while installing a column, all heaters should
be turned off and their respective zones allowed to cool
before touching the injector septum caps or any of the
fittings inside the oven.
This example uses a packed column. Before proceeding, determine whether the packed
column is in position 1 or 2 using the procedure previously described.
1. Open the oven door.
2. Turn on the Clarus GC, if it is not already on, and wait for the following screen to appear:
OVEN DOOR OPEN
Press CE to Continue
3. Press [CE].
Method 1
Ovn
206
OVN OFF
55
Notice that as the oven cools down, the actual temperature is continuously updated on the
bottom line.
4. Wait for the oven fan to turn off.
The oven fan automatically turns off when the oven temperature drops to 40 C.
5. Connect a soap bubble flowmeter to the packed injector fitting inside the oven.
To minimize the possibility of melting the tubing, we recommended using Tygon tubing
to make the connection.
Note:
The flow of carrier gas through a packed injector is controlled by the flow control knob on
the pneumatics control panel (see the following figure).
Packed Injector Fitting
Figure 39 A packed injector fitting.

6. Turn on the carrier gas at the tank and adjust the line pressure to 90 psig. (Adjust the inlet
pressure to 45 psig if you are using hydrogen as the carrier gas.)
207
System Utilities
7. Turn the flow control knob fully clockwise until it is completely closed.
8. Press [System] [System] [Enter].
The Stopwatch screen appears:
Stopwatch Flow
0.00 min Vol 1
Ideally, it should be zero, but some flow controllers may produce a small flow when
turned off.
10. Press [CE] to reset the stopwatch.
11. Press [System] [Enter] to enter the configuration mode. Using the [Carrier Prog] key,
select the appropriate screen.
Gas Display 2 Config
None kPa psig Flow
12. Press the [->Set] key to move the cursor to Flow, if it is not already there.
13. Press [Enter]
Carrier Gas 2 Config
Calibrate Flow ? No
14. Press [On/Yes 1].
Carrier Gas 2 Config
Calibrate Flow ? Yes
15. Press [Enter].
Carrier Gas
He
N2
H2
Config
Ar/CH4
16. Select the carrier gas you are using, then press [Enter].
208

Calib.
LO=0
Flow 2
HI=100
He
17. Type the flow value measured in step 9, then press [Enter].
18. Turn the flow control knob counterclockwise to start the carrier gas flowing.
19. Measure and adjust the flow to one of the following:
If a 0 to 100 mL/min flow element is installed: 100 10 mL/min
If a 0 to 20 mL/min flow element is installed: 20 2 mL/min
20. Repeat steps 11 through 19.

Calib.
LO=0
Note:
Flow 2
HI=100
He
The element symbol on the above screen is that for the carrier gas selected in step
16.
21. Select HI, then press [Enter].
Calib.
LO=0
Flow 2
He
HI=100
22. Type the flow just measured, then press [Enter] [Status Escape].
209
System Utilities
Printing the Run Log

To print the run log:
1. Press [System].
System Control
Confg PPC Lock >
System Control
Stpwtch Extrn Prnt>
2. Select Prnt, then press [Enter].

Print
Confg
System
Runlog
3. Select Runlog, then press [Enter].

Print
System
No Once Always
210
Selecting Once prints the most recent run log.
Selecting Always prints the run log after each run is terminated.
Selecting No cancels Always.
Printing the System Configuration

To print the system configuration:
1. Press [System].
System Control
Confg PPC Lock >
System Control
Stpwtch Extrn Prnt>
2. Select Prnt, then press [Enter].

Print
Confg
System
Runlog
3. Select Confg, then press [Enter].

The system configuration will be printed.
211
System Utilities
Locking and Unlocking the Keyboard

To lock or unlock the keyboard:
1. Press [System].
System Control
Confg PPC Lock >
System Control
Stpwtch Extrn Prnt>
2. Select Lock, then press [Enter].

Lock Keyboard
Enter Code
3. Enter a 0 to 4 digit code, then press [Enter]. This code (if entered) must be entered again
to unlock the keyboard.
If the keyboard is already locked, selecting Lock from the System Control menu displays
the following:
Lock Keyboard
Enter Code
To unlock the keyboard, enter the code, then press [Enter].
Note:
When the keyboard is locked, the function and parameter keys are read-only. Methods and
configuration may be displayed but not altered. If you forget the code, the instrument must
be turned off and then on again to free the keyboard. If external computer control is
activated, the keyboard is locked by the computer. You need not enter any code to lock the
keyboard. Just pressing [Enter] will lock the keyboard. If you lock the keyboard by pressing
[Enter], pressing [Enter] will unlock it.
212
Calibrating the Oven Temperature

The Clarus GC oven temperature is controlled by a sophisticated software routine that
permits adjustment of the actual oven temperature inside the oven up or down within a 10
C window. This calibration utility is intended for applications which require precisely
matching oven temperatures across several Clarus GCs, such as the determination of retention
indices. The calibration information is stored in a reserved area of the battery-backed
memory.
Required Equipment: A calibrated precision platinum resistance thermometer with
0.01 C readout and a probe capable of insertion into the GC oven.
The following steps summarize how to calibrate the oven temperature:
1. Calibrate the reference thermometer
2. Place the thermometer probe in the oven
3. Equilibrate the oven temperature
4. Enter the required offset value
5. Remove the thermometer probe
1.
Calibrate the Reference Thermometer

Calibrate your reference thermometer according to its instructions. If the
thermometer has been calibrated by an outside service, there is no reason to
recalibrate it yourself.
2.
Place the Thermometer Probe in the Oven
CAUTION
The thermometer probe must be placed as close as possible to the same

position in each GC oven to be calibrated. Access to the oven is provided
on the left-side oven wall.
213
System Utilities
1. Turn off the power and allow the oven to cool.

2. Remove the left-side instrument cover.
Note the location of three approximately 1-inch diameter holes that correspond to the holes
on the left side of the oven. One or more of these holes may be occupied by gas sampling
valves.
Figure 40 Left panel removed to reveal left side of the oven exterior.
3. Insert the temperature probe through the exposed white insulation covering one of the
holes so that the probe tip is positioned in the center of the oven cavity.
Note which hole you used and measure the length of the probe that protrudes into the
oven. Use the same position for subsequent oven calibrations.
214
Packed Injector Fitting
Figure 41 Holes on the left side of the oven interior.
3.
Equilibrate the Oven Temperature

1. Close the oven door, then turn the GC and thermometer on.
2. Set an oven temperature of 100 C or use another temperature if desired.
3. For best accuracy, set the detector and injector heaters to their normal operating
temperature.
4. Press [System].
System Control
Confg PPC Lock >
5. Select Confg, then press [Enter].
6. Press [Oven Prog] [Enter].
Oven Temp
Config
Calibrate ? No
7. Press [On/Yes 1].
The Oven Temp Calibrate screen appears:
Oven Temp
Calibrate
100.00
0.00
215
System Utilities
The above screen shows the time-averaged actual oven temperature in the upper right,
and the current temperature offset in the lower right.
8. Allow the oven temperature to equilibrate for at least 30 minutes. The displayed
temperature will approach 100.00 C (or the oven temperature you entered in step 2),
and the thermometer readout will approach a value close to 100.00 C.
4.
Enter the Required Offset Value

1. After the temperature has stabilized, subtract the thermometer reading from the actual
oven temperature shown on the previous screen.
2. Type this value into the above screen, then press [Enter]. For example, if the
thermometer reads 101.55 C, and the oven temperature reads 100.10 C, type a
value of -1.45 C.
Oven Temp
Calibrate
5.
100.10
-1.45
Remove the Thermometer Probe

After temperature calibration is satisfactory:
1. Open the oven door and allow the oven to cool until the fan stops.
2. Remove the temperature probe.
3. Fill in any hole left by the probe in the oven insulation.
4. Replace the left-side instrument cover.
216
Deconfiguring and Configuring Injectors

Occasions may arise when you may not be using one of the injectors for an extended period
of time. Instead of turning off the injector heater, you may find it more convenient to
"deconfigure" the unused injector. When you do this, the injector temperature screen for the
deconfigured injector will not appear in the method.
Every Clarus GC purchased has been configured at the factory for the specific injector(s) that
have been installed. You can check the injector configuration of your Clarus from the
Configuration Mode.
To enter the Configuration Mode:

1. Press [System].
System Control
Confg PPC Lock >
2. Press [Enter].
Display the configuration for injector 1 by pressing [Inj Prog].
For example, if injector 1 has been configured as a capillary injector, the following
appears:
Injector 1
Config
None Pkd Cap GSV
217
System Utilities
To deconfigure this injector:

1. Select None.
Injector 1
Config
None Pkd Cap GSV
2. Press [Enter].
As a result of the deconfiguration, injector 1 is removed from the method and its
injector temperature screen will no longer appear in the method.
To restore the configuration:

1. Select Cap, then press [Enter].
218
Deconfiguring and Configuring Detectors

Occasions may arise when you may not be using one of the detectors for an extended period
of time. Instead of turning off the detector heater, you may find it more convenient to
"deconfigure" the unused detector. When you do this, the detector temperature screen for the
deconfigured detector will not appear in the method.
Every Clarus GC has been configured at the factory for the specific detector(s) that have been
installed. You can check the detector configuration o from the Configuration Mode.
To enter the Configuration Mode:

1. Press [System].
System Control
Confg Lock >
2. Press [Enter].
Regardless of the screen that appears, you can display the configuration for detector 1 by
pressing [Detect Control].
219
System Utilities
For example, if detector 1 has been configured as an FID, the following screen appears:
Detector 1 Config
FID
Output
To deconfigure this detector:
1. Select Output, then press [Enter].
The screen appears as shown below:
Detector 1 Config
FID
Output
2. Press [Enter].
As a result of the deconfiguration, detector 1 is removed from the method and its detector
temperature screen will no longer appear in the method.
Note:
If one of the detectors has been deconfigured, analog data from the remaining detector will
be routed to both output channels. Both detectors should not be deconfigured at the same
time.
To restore the configuration:

?
220
Follow the above steps to enter the configuration mode. Choose [Detect Control], select
FID, then press [Enter] [Status Escape].
Appendix:
Configuration Menus
The menu examples in this appendix were prepared with a Clarus equipped with the
autosampler and the following detectors and injectors:
An FID in detector position 1 (front)
An ECD in detector position 2 (rear)
A capillary injector in injector position 1 (front)
A packed injector in injector position 2 (rear)
The Clarus used also has an integrator connected to Output 1 and a recorder connected to
Output 2.
223
Appendix: Configuration Menus
Displaying Configuration Menus

Configuration Menus are displayed from the Configuration Mode. To enter the
Configuration Mode:
1. Press [System].
System Control
Config
Lock
>
2. Press [Enter].
The first configuration menu appears:
None Autosamp
You can display the configuration menus for your system sequentially by pressing
[Enter] each time you wish to move from one menu to the next. Notice that the menus
are on a loop, i.e., after displaying the last menu, pressing [Enter] redisplays the first
menu.
The following section shows examples of configuration menus.
224
Configuration Menu Examples

Single Multi Off
A/S Syringe
Config
0.5L 5.0L 50L
Auto Program
Auto Resume
Config
Off
Oven Maximum
Temp Limit
Oven Temp
Calibrate ?
Config
No
Oven
Config
Equil. Time
2.0m
Config
CO2
Injector 1
Config
None Pkd Cap GSV
Coolant
None
LN2
Injector 2
None Pkd
Config
350
Config
Cap GSV

None kPa psig Flow

None kPa psig Flow
Valve 1
Config
None Valv Split GSV
Valve 2
Config
None Valv Split GSV
Valve 3
Config
None Valv Split GSV
Valve 4
Config
None Valv Split GSV
Detector 1
FID Output
Config
FID 1 Filter Config

50 200 800
Detector 2
ECD Output
Config
ECD 2 Filter Config

200 800
Aux Heater Config

None
Enable
Output 1
Config
Recorder Integrator
Output 2
Config
Recorder Integrator
225
Integrator 1
Offset
Detector 2
ELCD
Extn
Config
0.5mV
Config
Output
Recorder
Offset
Config
5.0 %
ELCD 2
Config
Heat Detector
No
Depending on the menu and the item selected, additional menus may appear. These have
been previously described where appropriate.
* The Aux(iliary) Heater is reserved for use with PerkinElmer supplied accessories.
The menu does not appear if a TCD is configured into the system.
If a TCD is installed, the "Aux Heater" is configured as TCD:

Aux Heater
Config
None
Aux TCD
226
Going Directly to a Primary Configuration Menu

You can go directly to most configuration menus by first pressing [System] [Enter], then
pressing the appropriate key as shown in the following table.
Press this Key:
Oven Maximum Temp Limit Setting
[Oven Prog]
[Oven Prog] [Enter]
[Time]
Coolant Type
[Rate]
Real Time Clock
[Time] [Enter]
Injector Type
[Inject Prog]
Detector Settings
[Detect Control]
[Output]
Output Offset
[Auto Zero]
Autosampler Mode
[Auto]
Pressing a parameter key multiple times allows you to step through the options for that key.
For example, press [Detect Control] twice to see the options for the second detector, if
installed.
227
228
Index
A
Abbreviations, screen, 13
About
the keyboard, 26
Active Method
editing, 129
parameters
editing, 129
examples, 128
viewing, 126
Adjusting
carrier gas pressure, 138
Attenuating
detector signal, 148, 149
Auto-ignition, FID, 66
Autosampler
configuring, 54
configuring syringe size, 55
controlling, overview, 167
Function key, 30
run
pausing, 187
resuming, 187
stopping, 188
starting, 177, 181
tasks
cleaning the syringe, 185
pausing autosampler run, 187
resuming autosampler run, 187
tower, parking, 188
tray, 167
turntable, 167
using with TCD, 107, 192
vials, waste & wash, 190
Autozeroing a detector, 151
B
Background Calibration Menu, 196
Background calibration options
multi, 197
off, 197
Index
once, 196
Background compensation
calibrating baseline profile, 196
glossary, 16
overview, 195
turning off, 198
turning on, 198
Background menu, 196
Balancing TCD bridge current, 106
Baseline profile, calibrating, 196
Bridge current vs. range, 106
C
Calibrating
baseline profile, 196
optional flow readout, 206
oven temperature, 213, 216
reference thermometer, 213
CAP, abbreviation, 13
Carrier gas
checking status, 42
configuring pressure display for manual
pneumatics, 52
Carrier gas pressure
adjusting, 138
configuring display for manual pneumatics, 52
displaying, 138
viewing, 138
Changing
detector temperature, 141
injector temperature, 137
TCD polarity, 145
Chromatographic terms, glossary, 17
Clarus
controlling, 125
Cleaning the syringe, 185
Clock, setting, 60
Cmptr, abbreviation, 13
Combustion
control valves, FID, 81
needle valves, FID, 81
Configuration
displaying menus, 51
entering, 53
printing, 211
Configuration Menus
displaying, 204
Configuration Mode
entering, 204
230
escaping, 126
Configuring
autosampler, 54
clock, 60
detectors, 219
equilibration time, 131
injectors, 62, 217
integrator, 69
Integrator/Recorder offsets, 70
manual pneumatics carrier gas pressure display,
52
multi program mode, 178
oven, 56
printer, 71
recorder, 69
startup time, 60
valves, 65
Control key
Delete, 32
Run, 31
Control valves
combustion, 81
Conventions, 13
Copying a Method, 162
Ctrl, abbreviation, 13
D
Deconfiguring
detectors, 219
injectors, 217
Delete control key, 32
Deleting
a Stored Method, 162
timed event, 156
Detector
attenuating
signal to a recorder, 148
signal to an integrator, 149
autozeroing, 151
configuring, 66, 219
cover, 78
heater
turning off, 141
turning on, 142
output
rerouting, 146
rerouting using a timed event, 147
routing, 146
temperature

changing, 141
displaying, 140
setting, 140
Detector temperature
checking status, 42
Displaying
carrier gas pressure, 138
timed events table, 155
E
ECD
abbreviation, 13
adjusting make-up gas, 100
outlet, 97
overview, 93
setting up, 96
setting up manual pneumatics, 99
setup summary, 96
venting the outlet, 96
Entering parameters
single program mode, 175
Entry keys, 33
Off/No, 33
On/Yes, 33
Equil, abbreviation, 13
Equilibration
screen, 40
Equilibration time
configuring, 131
Extrn, abbreviation, 13
F
FID
abbreviation, 13
adjusting air flow, 83
adjusting hydrogen flow, 81
attaching a flowmeter, 78
auto-ignition, 66
cross sectional view, 77
range changing, 143
range setting, 142
Flow controller
See optional flow readout:, 206
Flow readout, calibrating, 206

Flowmeter
attaching to a TCD, 104
attaching to an ECD, 98
attaching to an FID, 78
Function key
auto(sampler), 30
Method, 29
System, 29
Function keys
description of, 28
G
GC tasks vs. parameter keys, 127
GC temperature program steps, 130
Gen, abbreviation, 13
Generated Method
saving, 160
setting up, 160
Ghost Peaks, 17
Glossary
autosampler terms, 15
chromatographic terms, 17
GSV, abbreviation, 13
H
Hydrogen flow
adjusting, 81
I
Inj, abbreviation, 13
Inj/vial, abbreviation, 13
Injector heater
turning off, 137
turning on, 138
Injector temperature
changing, 137
checking status, 41
displaying, 137
setting, 136
Injectors
configuring, 62, 217
Inlet temperature program
setting up, 130
Int, abbreviation, 13
Integrator
231
Index
configuring, 69
Integrator noise, 149
Isothermal temperature program
setting up, 131
K
Key
Autosampler function, 30
Method function, 29
parameter, 34
System function, 29
Keyboard
about the, 26
locking, 212
unlocking, 212
kPa, abbreviation, 13
L
Leaving
timed events screen, 155
Locking the keyboard, 212
M
Make-up gas
adjusting for an ECD, 100
control valve, 99
needle valve, 99
Menu
about, 44
auto(sampler), 30
background, 196
background calibration, 196
escaping from, 45
Injector, 62
Output, 69
printer, 71
selecting an option, 44
System Control, 29, 53, 201, 204
Menu, overview, 37
Method
copying, 162
printing, 164
setting up, 177
Method function key, 29
Method Menu, 159
Method utilities+, 159
Mode
232
configuration, 204
Multi program mode
configuring, 178
entering parameters, 179
running samples, 178
Multiprogram mode, 170
Multi-ramp temperature program
setting up, 135
N
NPD
adjusting the air flow, 114
adjusting the hydrogen flow, 113
bead activation, 116
reactivating a used bead, 121
setting up manual pneumatics, 111, 112
NPD, abbreviation, 13
O
Off/No entry key, 33
Offset screen, 70
Offsets
configuring Integrator/Recroder offsets, 70
On/Off Switch, 38
On/Yes entry key, 33
OnCol, abbreviation, 13
One-ramp temperature program
setting up, 133
Option, selecting from a menu, 44
Optional flow readout, calibrating, 206
Output Menu, 69
Oven
calibrating the temperature, 216
calibrating the temperature,, 213
checking temperature status, 41
configuring, 56
setting a heating delay time, 59
setting equilibration time, 56
turning on, 102
Oven temperature program
setting up, 130
setting up a multi-ramp, 135
setting up a one-ramp, 133
setting up isothermal, 131
Overview
AutoSystem XL GC, 23
ECD, 93
TCD, 101

Ovn, abbreviation, 14
P
Parameter keys, 34
method, 126
Parameter screens, 126
Parameters
Active Method
examples, 128
viewing, 126
injection mode, 172
syringe wash, 171
Parking, autosampler tower, 188
Paus, abbreviation, 14
Pkd, abbreviation, 14
POC
configuring, 62
Inlet Programmed Mode, 62
Oven Programmed Mode, 62
Pre
See syringe wash parameters, 171
Pre, abbreviation, 14
Pres, abbreviation, 14
Pressure display, configuring for manual
pneumatics, 52
Prg, abbreviation, 14
Pri, abbreviation, 14
Printer
configuring, 71
menu, 71
Printing
Configuration, 211
run log, 210
Priority sample, inserting, 188
Psi, abbreviation, 14
psig, abbreviation, 14
PSS
configuring, 62
Inlet Programmed Mode, 62
Oven Programmed Mode, 62
Pump
See syringe wash parameters, 171
R
Recorder
configuring, 69
Rerouting
detector output, 146

Resm, abbreviation, 14
Routing
detector output, 146
Run control key, 31
Run log
printing, 210
Running samples
single program mode, 174, 177, 182
S
Saving
Generated Method, 160
Screen
abbreviations, 13
Clock, 60
equilibration, 40
Offset, 70
Sleep Time, 57
stopwatch, 202
Syringe Wash, 171
timed events, 152
leaving, 155
Screens
about, 46
changing values, 46
Screens, overview, 37
Septum Purge Mode (PPC)
viewing/setting, 139
Set entry key, 33
Setting
FID range, 142
TCD range, 144
Setting up
Generated Method, 160
isothermal temperature program, 131
multi-ramp temperature program, 135
one-ramp temperature program, 133
PPC valves, 140
Stored Method, 161
Setup summary
ECD, 96
FID with manual pneumatics, 78
NPD with manual pneumatics, 112
TCD, 102
Single program mode, 170
233
Index
entering parameters, 175
running samples, 174
Sleep Time
creating a sleep method, 57
setting, 57
Startup time, setting
configuration, 60
Status
system, 39
Status checking
carrier gas, 42
oven temperature, 41
Status, overview, 37
Stopping, autosampler run, 188
Stopwatch
setting, 202
Stored Method
deleting, 162
setting up, 161
Stpwtch, abbreviation, 14
Syringe
cleaning, 186
configuring autosampler syringe size, 55
Syringe tower, 167
Syringe wash
parameters, 171
screen, 171, 183, 184
System Control Menu, 29, 53, 201, 204
System function key, 29
System status, 39
System utilities, 201, 220
System, turning on, 38
T
TCD
abbreviation, 14
attaching a flowmeter, 104
balancing the bridge, 106
overview, 101
234
polarity
changing, 145
range
setting, 144
range vs. bridge current, 144
using with autosampler, 107, 192
Temperature program
isothermal
setting up, 131
setting up a multi-ramp, 135
setting up a one-ramp, 133
Temperature program steps, 130
Temperature Programming, 18
Timed event
adding, 154
deleting, 156
entering, 152
Timed events screen, 152
leaving, 155
Timed events table
building, 151
displaying, 155
editing, 156
going directly to a line, 156
Tray, autosampler, 167
Turntable, autosampler, 167
U
Unlocking the keyboard, 212
Utilities, system, 201, 220
V
Valves
combustion, FID, 81
configuring, 65
Valves (PPC)
setting up, 140
PerkinElmer
710 Bridgeport Avenue
Shelton, CT 06484-4794, U.S.A.
Internet: http://www.perkinelmer.com
email: info@perkinelmer.com
PerkinElmer is a registered trademark of PerkinElmer, Inc.

Manual Equipo Clarus400-480

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Escaping from a Menu ........................................................................... 45

Other Requirements ............................................................................... 91

Building a Timed Events Table ........................................................... 151

Calibration Menu Options ................................................................... 196

Clarus 400/480 GC Software Guide

About This Manual

The manual consists following chapters:

Introducing the Clarus 400/480 GC describes the Clarus GC

System Description describes the Clarus GC and its major

Initial Setup Procedures contains configuration procedures that

Setting Up Detectors contains subsections that describe how to

Controlling the Clarus 400/480 GC describes how to set

Controlling the Autosampler describes autosampler screen

Background Compensation describes how to set the background

System Utilities contains procedures for using the built-in

Examples of Configuration Menus.

Clarus 400/480 GC Software Guide

Manual Conventions and Screen Abbreviations

Clarus 400/480 GC Software Guide

Glossary of Clarus GC Terms

Washing the syringe.

The number of prewashes of sample to prime the syringe (no

The number of post injection syringe washes with a solvent.

The number of times the syringe draws up sample and

The style of injection.

Fast speed of the syringe during sample injection. This is used

Normal speed of the syringe during sample injection.

Slow speed of the syringe during sample injection in order to

The number of solvent washes performed before the

The number of seconds the plunger pauses when drawing up a

A routine that automatically subtracts a stored calibrated

Changing the oven temperature as quickly as possible to reach

The detector output signal when no components are being

A method in which the oven temperature remains constant

A collection of parameters that control the GC.

A timed event that you set to occur before the instrument

An independent variable used to specify a condition to be met.

The time after equilibration during which negative-time events

For a Flame Ionization Detector, range means amplification of

Indicates that all method parameters have reached their set

The time from sample injection to the end of the oven

The GC can be set to a predefined method for gas savings.

Events that take place before or during a GC run as

A heated area in the GC oven, injector, or detector.

Clarus 400/480 GC Software Guide

Glossary of Chromatographic Terms*

Reference: Denney, R.C. A Dictionary of Chromatography.

Clarus 400/480 GC Software Guide

Symbols Located on the Clarus 400/480 GC

Clarus 400/480 GC Software Guide

Figure 1. The Clarus GC.

Overview of the Clarus 400/480 GC

Nitrogen Phosphorus (NPD)

Clarus 400/480 GC Software Guide

Figure 2. Example of a dual-channel pneumatics control panel in the Clarus GC.

About the Keyboard

Figure 3. The Clarus 400/480 GC keyboard.

Clarus 400/480 GC Software Guide

About the Screen

Figure 4. Vacuum fluorescent screen.

Function Key Descriptions