Instrument-dependent parameters vary from instrument to instrument.

Within each
instrument, the values are constant between components, though they have a tendency to
drift over time. On installation, and periodically after that, they must be optimized for the
instrument. Instrument-dependent parameters are:

Resolution parameters (ion energy, resolution offset values)

Mass calibration values (mass and DAC values)

Detector parameters (CEM, deflector)

Resolution and mass-calibration parameters are stored as instrument data and can be
optimized in the Tune Method Editor window.

Source-dependent parameter :
Optimal source-dependent parameter values depend on the LC conditions. Sourcedependent parameters are therefore optimized at or near the desired LC flow conditions
using split infusion or FIA.
The positioning of the probe in the source can have a significant impact on the sensitivity
of the analysis. For more information on how to optimize the position of your probe, refer
to the appropriate ion source operators manual.
These parameters may change depending on the source you are using. Examples are as
follows:
GS1 (Gas 1): The GS1 parameter controls the nebulizer gas. The nebulizer gas helps
generate small droplets of sample flow and affects spray stability and sensitivity. (This
parameter is called nebulizer gas for API 3000 systems.)
Neb (Nebulizer Gas): The Neb parameter controls the nebulizer gas. The nebulizer gas
helps generate small droplets of sample flow and affects spray stability and sensitivity.
(This parameter is called Gas 1 for all instruments other than API 3000 systems.)
GS2 (Gas 2): The GS2 parameter controls the auxiliary, or turbo, gas. It is used to help
evaporate the spray droplets and prevent solvent from entering the instrument. (This
parameter is called auxiliary, or turbo, gas for API 3000 systems.)
Aux (Auxiliary Gas): The Aux parameter controls the auxiliary, or turbo, gas. It is used to
help evaporate the spray droplets and prevent solvent from entering the instrument. (This
parameter is called Gas 2 for all instruments other than the API 3000 system.)
TEM (Temperature): The TEM parameter controls the temperature of the turbo gas in
the TurboIonSpray source, or the temperature of the probe in the heated nebulizer (or
APCI) source. It is used to help evaporate the solvent to produce gas phase sample ions.
For recommended starting temperatures for these two sources, see TIS Temperature and
Solvent Composition and APCI Probe Temperature and Solvent Composition.

CUR (Curtain Gas Interface): The CUR parameter controls the gas flow of the Curtain
Gas interface. The Curtain Gas interface is located between the curtain plate and the
orifice. It prevents solvent droplets from entering and contaminating the ion optics. The
gas flow should be maintained as high as possible without losing sensitivity.
IS (IonSpray Voltage): The IS parameter controls the voltage applied to the needle that
ionizes the sample in the ion source. It depends on the polarity, and it affects the spray
stability and sensitivity.
IS (Ion Transfer Voltage): For the PhotoSpray source, the IS parameter controls the
voltage that transfers the ions from the primary ionization region towards the curtain
plate orifice.
ihe (Interface Heater): The ihe parameter switches the interface heater on and off.
Heating the interface helps maximize the ion signal and prevents contamination of the ion
optics. The interface plate is heated to 100 C. (This parameter does not apply to
API 150EX and API 3000 systems.)
IHT (interface heater temperature): The IHT parameter controls the temperature of the
NanoSpray interface heater and is only available if the NanoSpray source and interface is
installed. The temperature can be adjusted up to 250 C. (This parameter does not apply
to API 2000, API 3000, and Q TRAP systems.)
NC (Nebulizer, or Needle, Current): The NC parameter controls the current applied to
the corona discharge needle in an APCI source, also known as heated nebulizer source.
The discharge ionizes solvent molecules, which in turn ionize the sample molecules.
svp: The svp parameter controls the selection of the DuoSpray source probe:
TurboIonSpray or heated nebulizer. It only appears if you have the DuoSpray source
installed. In the parameter settings file, the options are 1 for TurboIonSpray and 2 for
heated nebulizer.

compound-dependent parameters:
The compound-dependent parameters consist mostly of lens elements in the ion path.
Optimal values for compound-dependent parameters vary depending on the compound
being analyzed. Not all parameters will appear for all instruments. If a parameter is in
fixed-mode, it does not appear in the Manual Tune window and the Acquisition Method
Editor and cannot be manually set. Although you can put the parameter in operator-mode
so it will appear, the default value in fixed-mode should be appropriate for most
situations. The following are examples of compound-dependent parameters, organized
according to their order in the ion path:
DP (Declustering Potential): The DP parameter controls the potential difference
between ground (usually the skimmer) and the orifice plate. It is used to minimize solvent

cluster ions, which may attach to the sample. The higher the voltage, the greater the
amount of fragmentation. If the declustering potential is too high, the sample ion itself
may fragment.
FP (Focusing Potential): (For API 2000 and API 3000 instruments only.) The FP
parameter controls the voltage applied to the focusing ring lens. The focusing potential
helps focus the ions through the skimmer region of the mass spectrometer interface. It
can induce fragmentation in the interface area, similar to the declustering potential.
EP (Entrance Potential). The EP parameter controls the potential difference between
the voltage on Q0 and ground. The entrance potential guides and focuses the ions
thorough the high-pressure Q0 region.
IQ1 (Focusing Lens 1): The IQ1 parameter controls the voltage on the first interquadrupole lens. By default, it is in fixed-mode.
Q0 Trapping: (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP instruments only.) The
Q0 trapping parameter controls the storage of ions in the Q0 region. It is used to increase
sensitivity by storing ions in the Q0 region while ions are being mass-selectively ejected
from the LIT.
ST (Prefilter): The ST parameter controls the voltage applied to the prefilter. It is used
to focus the ions into Q1. By default it is in fixed-mode.
IE1 (Ion Energy 1): The IE1 parameter controls the potential difference between Q0
and RO1. Although this parameter does affect the sensitivity, it has a greater impact on
peak shape, and it is considered a resolution parameter. IE1 is used in Q1 and MS/MStype scans. In Q3 scans, the potential applied to Q1 is called RO1 (Q1 rod offset) and
helps to transmit ions.
RO1 (Q1 Rod Offset): The RO1 parameter controls the voltage on the first analyzingquadrupole (Q1). It is used only in Q3 scans. By default, RO1 is in fixed-mode. In Q1
and MS/MS-type scans, the potential applied to Q1 is called IE1 (Ion Energy 1).
CEP (Collision Cell Entrance Potential): (For API 2000, API 3200, Q TRAP, and 3200
Q TRAP instruments only.) The CEP parameter controls the collision cell entrance
potential, which is the potential difference between Q0 and IQ2. It focuses ions into Q2
(collision cell). CEP is used in Q1, MS/MS-type, and LIT scans. Note that for Q3 scans,
this voltage is called IQ2 and by default is in fixed-mode.
IQ2 (Focusing Lens 2): (For API 3000, API 4000, API 5000 and 4000 Q TRAP
instruments only.) The IQ2 parameter controls the collision cell entrance potential, which
is the potential difference between Q0 and IQ2. It focuses ions into the Q2 (collision
cell). By default, it is in fixed-mode.

RO2 (Collision Cell Rod Offset): The RO2 parameter controls the voltage applied to
Q2 (collision cell). It is used only in Q1 and Q3 scans, where it transmits the ions toward
the detector. In MS/MS-type scans, the voltage applied to the collision cell is accessed
through the CE (collision energy) parameter.
CE (Collision Energy): The CE parameter controls the potential difference between Q0
and Q2 (collision cell). It is used only in MS/MS-type scans. This is the amount of energy
that the precursor ions receive as they are accelerated into the collision cell, where they
collide with gas molecules and fragment. In Q1 and Q3 scans, the voltage applied to the
collision cell is RO2 (collision cell rod offset).
CAD (Collision Gas): The CAD parameter controls the pressure of collision gas in the
collision cell during Q3 MS, MS/MS-type, and LIT scans. For Q3 MS scans, the collision
gas helps to focus the ions as they pass through the collision cell; by default, this
parameter is in fixed mode. For MS/MS-type scans, the collision gas acts as a target to
fragment the precursor ions. When the parent ions collide with the collision gas, they can
dissociate to fragment ions. For LIT scans, the collision gas helps to focus and trap ions
in the LIT.
CES (Collision Energy Spread): (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP
instruments only.) The CES parameter controls the spread of collision energies used
when filling the LIT and applies when you are using the AutoFrag feature. It is used in
conjunction with the Collision Energy (CE) parameter.
TDF CE (Time Delayed Fragmentation Collision Energy): (For Q TRAP, 3200 Q
TRAP, and 4000 Q TRAP instruments only.) The TDF CE parameter controls the
potential difference between RO2 and RO3 for TDF (Time Delayed Fragmentation)
scans. This is the amount of energy that the precursor ions receive as they are accelerated
into Q3, where they collide with gas molecules and fragment.
Q3 Cool Time: (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP instruments only.) The
Q3 Cool Time parameter controls the amount of time that the precursor ions are allowed
to cool prior to collection of their fragment ions in TDF (Time Delayed Fragmentation)
scans.
CXP (Collision Cell Exit Potential): The CXP parameter controls the potential
difference between RO2 and IQ3 (for API 2000, API 3200, Q TRAP, and 3200 Q TRAP
instruments) or between RO2 and ST3 (for API 3000, API 4000, API 5000, and 4000 Q
TRAP instruments). It is only used in Q3 and MS/MS-type scans, where it transmits the
ions into Q3. In Q1 scans, the voltage applied to IQ3/ST3 is accessed through the IQ3 or
ST3 parameters.
IQ3 (Focusing Lens 3): (For API 2000, API 3200, Q TRAP, and 3200 Q TRAP
instruments only.) The IQ3 parameter controls the voltage applied to IQ3 (focusing lens
3). It is only used in Q1 scans, where it transmits the ions into Q3. By default, IQ3 is in

fixed-mode. In Q3 and MS/MS-type scans, the voltage applied to IQ3 is accessed through
the CXP (collision cell exit potential) parameter.
ST3 (Prefilter 3): (For API 3000, API 4000, and API 5000 instruments only). The ST3
parameter controls the voltage applied to ST3 (prefilter 3). It is only used in Q1 scans,
where it transmits the ions toward the detector. By default, ST3 is in fixed-mode. In Q3
and MS/MS-type scans, the voltage applied to ST3 is accessed through the CXP
(collision cell exit potential) parameter.
IE3 (Ion Energy 3): The IE3 parameter controls the potential difference between RO2
and RO3. Although this parameter does affect the sensitivity, it has a greater impact on
the peak shape, and it is considered a resolution parameter. IE3 is used in Q3 and
MS/MS-type scans. In Q1 scans, the potential applied to Q3 is called RO3 (Q3 rod offset)
and helps to transmit ions.
RO3 (Q3 Rod Offset): The RO3 parameter controls the voltage on the second analyzing
quadrupole (Q3). It is used only in Q1 scans. By default, RO3 is in fixed-mode. In Q3
and MS/MS-type scans, the potential applied to Q3 is called IE3 (Ion Energy 3).
Q3 Entry Barrier: (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP instruments only.)
The Q3 Entry Barrier parameter controls the potential difference between RO2 and RO3.
It is used to transfer the ions from Q2 into the LIT.
AF2 (Excitation Energy): (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP instruments
only.) The AF2 parameter is the peak-to-peak voltage of the auxiliary frequency (Aux
RF) applied to Q3 during MS/MS/MS scans. It is used to fragment the isolated second
precursor ion.
MS/MS/MS Fragmentation Time: (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP
instruments only.) The MS/MS/MS Fragmentation Time parameter controls the amount
of time that the excitation energy is applied in MS/MS/MS scans. It is used in
combination with the excitation energy to fragment the isolated second precursor ion.
MCS (Multi-Charge Separation) Barrier: (For 3200 Q TRAP, and 4000 Q TRAP
instruments only.) The MCS Barrier parameter controls the voltage used when
eliminating the singly-charged ions from the LIT in an EMC (Enhanced Multi-Charge)
scan.
Q3 Empty Time: (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP instruments only.)
The Q3 Empty Time parameter controls the amount of time that singly charged ions are
removed from the LIT in an EMC (Enhanced Multi-Charge) scan.
Fixed LIT Fill Time: (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP instruments only.)
The Fixed LIT Fill Time parameter controls amount of time that the LIT fills with ions.

DFT (Dynamic Fill Time): (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP
instruments only.) The DFT parameter controls whether the LIT fill time is dynamic or
fixed. If DFT is turned on, the software will dynamically calculate the length of time that
ions are collected in the LIT based on the incoming ion signal.
EXB (Exit Barrier): (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP instruments only.)
The EXB parameter controls the voltage on the exit lens. It is used in LIT scans to massselectively eject ions from the LIT. It affects the peak width, the peak shape, and the
intensity of the ion signal.
AF3 (Trap RF Amplitude): (For Q TRAP, 3200 Q TRAP, and 4000 Q TRAP
instruments only.) The AF3 parameter controls the zero-to-peak voltage of the auxiliary
frequency (Aux RF) applied to Q3 when scanning the ions out of the LIT. The AF3
parameter affects the peak width, the peak shape, and the intensity of the ion signal.
C2B (Collar 2 Barrier): (For Q TRAP and 3200 Q TRAP instruments only.) The C2B
parameter controls the voltage applied to the collar lens. It affects the peak width, the
peak shape, and the intensity of the ion signal.

Resolution parameters:
Resolution parameters are the instrument-dependent parameters that affect the resolution,
sensitivity, and peak shape, and depend on the type of scan. For example, for a Q1 scan:
Ion energy 1 (IE1). Increasing this value increases the sensitivity but broadens peaks for
Q1 scans.
Q1 resolution. This is the resolution for Q1 or precursor ion scans.
and for a Q3 scan:
Ion energy 3 (IE3). Increasing this value increases the sensitivity but broadens peaks for
Q3 and MS/MS scans.
Q3 resolution. This is the resolution for Q3 or product ion scans.
The parameters currently in use appear on the Resolution tab of the Tune Method Editor
window.

Detector parameters:
Detector parameters are the instrument-dependent parameters that affect the detector.
They are:
CEM (CEM): The CEM parameter controls the voltage applied to the detector. It is used
to detect ions.
DF (Deflector): The DF parameter controls the voltage applied to the deflector. It is used
to direct ions into the detector. By default it is in fixed mode.
The parameters currently in use appear on the Detector tab of the Tune Method Editor
window.

-----------------*-----------------*----------------*--------------*---------*----------*--------------The quantity and type of sample affects the optimal TIS temperature. At higher flow rates
the optimal temperature increases. A more significant factor is the composition of the
solvent. As the organic content of the solvent increases, the optimal probe temperature
should decrease.
The TIS probe is normally used with sample flow rates of 40 to 1000 L/min. The heat is
used to increase the rate of evaporation and this improves ionization efficiency resulting
in increased sensitivity.
For starting temperatures, see the following table:
Recommended Starting Temperatures
Flow Rate
Temperature
120 L/min 100200C
20100 L/min
150350C
100300 L/min
300400C
300 L/min1 mL/min
400500C
Commonly Used Solvents and Modifiers
Commonly used solvents and modifiers are:

acetonitrile

methanol

propanol

water

acetic acid

formic acid

ammonium formate

ammonium acetate

The standard concentration of ammonium formate or ammonium acetate is from 2 to 10

mmol/L for positive ions and 2 to 50 mmol/L for negative ions. The concentration of the
organic acids is 0.1 to 0.5% by volume.
The following modifiers are not commonly used because they complicate the spectrum
with their ion mixtures and cluster combinations. They may also suppress the strength of
the target compounds ion signal.

TEA (triethyl amine)

sodium phosphate

TFA (trifluoroacetic acid)

SDS (sodium dodecyl sulfate)

The Resolution Optimization Options dialog box allows you to select the options to be
used by an automatic resolution optimization operation. To display this dialog box, on the
Tools menu, click Resolution Optimization.
Note: For time-of-flight (TOF) instruments, instrument and polarity parameters are readonly and display references from the calibration standard. You can adjust the Resolution
and Peak Search parameters.
Standard: Select the calibration standard from the list. A calibration standard is a wellcharacterized compound, such as positive PPG (
PPGs Pos.).
Quad 1/Quad 3: Select the quadrupole or quadrupoles on which the resolution will be
optimized. For TOF instruments, Quad 1 is displayed as read-only.
Resolution Parameters
Unit/High: Select the resolution. Usual criteria are:

For unit resolution, a peak width of 0.7 0.1 amu at 50% of the maximum peak
height.

For high resolution, a peak width of 0.5 0.1 amu at 50% of the maximum peak
height.
Peak Search Parameters
Search Range: Type or edit the value to set the range of the search for each mass. This
range should be kept small to allow automatic resolution to assign the correct peak. If this
is too wide, the Analyst software may choose the wrong peak.
Threshold: Type or edit the threshold, which is the value the peak must exceed to be
distinguished from background noise.
Polarity Parameters
Polarity: If the selected calibration standard can be used with both polarities, these
options will be available. Select Positive, Negative
, or both. If the selected calibration standard can be used with one polarity only, these
options are not available. In that case, they indicate the values taken from the reference
table for the selected calibration standard.
Edit: Click to display the current reference table.

Mass Calibration on Success: Select to perform a mass calibration automatically if the

resolution optimization is successful; that is, resolutions have been tuned to 0.7 0.1 amu
(unit) or 0.5 0.1 amu (high).
Update Mass Dependent Parameters: (Not available for TOF instruments.) Select to
update the values of any mass-dependent parameters. Realignment of the mass axis may
change the position of the peaks, so the mass-dependent parameters may need updating.
Overwrite Tune Acquisition Methods: Select to allow existing acquisition methods
maintained by Tune to be overwritten.