MS Lesson 4, How to Read a GC-MS Report and Find the [M]+:

The GC-MS data can be presented in different ways. Whatever the format, the essential
data remain the same. A standard GC-MS report is shown on the next page. The report
includes data from the GC chromatogram and data from the MS spectrum. The GC data
tells you how many compounds (qualitative information) were detected in the sample.
The GC data will also give you the quantitative data: the areas of peaks that are detected
in your sample are related to the amount of each compound in the sample. You can use
these peak areas to calculate percent purity of a sample based on GC analysis. The GC
data in a GC-MS report is used to determine the number and amount of the analytes that
pass through the chromatograph. In addition to GC data, the MS records a mass
spectrum for each compound, or peak in the GC. If there were five compounds (peaks)
detected in the GC, then there would be five MS spectra, one for each peak. Obviously,
this means that a GC-MS report will contain lots of information. Much of it is self-
explanatory.

The first step in evaluation of a GC-MS report is to look over the report to make sure that
the report you received is for the compound you submitted. Does the sample name
correspond to your name? If you see a string of ? characters instead of your name, then
that means that the GC-MS operator could not read your name from the log sheet. You
should always assume that the GC-MS operator does not know you or recognize your
name. Make sure that you print your name in block letters when you fill out the log
sheet. Is the miscellaneous information descriptive of the compound you thought you
were submitting for data collection?

Sometimes MS data is presented along with a computer Library Search Report. The PC
tries to match the spectrum of your analyte to one of the 50,000 spectra that are stored in
the PC MS library. The best fit may (or may not) be your compound. Searching against
the WILEY library (published by WILEY), the computer finds the most likely matches
and lists them. The degree of similarity between the MS spectrum of an analyte and the
spectrum of a known compound in the library is indicated as % Quality. A higher %
means a better match. A match quality of >95% indicates good similarity of the library
spectrum to the spectrum of the analyte being evaluated. But you must exercise caution
in looking over any library match report. The library may have more than one entry for
each compound. In addition, nomenclature used in the library database may not always
be the same for each entry or the same as the name that you are expecting.

Perhaps the most useful presentation of MS spectral data is a numerical data table. A
tabulation of the MS spectrum of 4-nitroacetophenone and the graphical presentation of
the same data are shown on the previous pages in this manual. The structural formula
will not be part of GC-MS reports that you receive for your samples. The tabulated data
is needed to determine intensities of ions detected at each mass/charge value. The
compound 4-nitroacetophenone, has a molecular formula of C8H7NO3. Since the
compound has an odd number of nitrogen atoms, its [M]+ has an odd value for
mass/charge.
As you look at the MS data presentations, you will immediately notice that MS spectra
have lots of peaks. Furthermore, each peak has two notable features: different m/z values
and different sizes (intensities). For the time being, we only need to consider one of the
peaks. That one peak is, of course, the molecular ion peak. If you know the structure of
the analyte, finding the [M]+ should be easy, provided that the compound is one of the
85% of organic compounds that has molecular ions in electron impact MS spectra.
Calculate the expected m/z value and then look for it. It is, of course, more difficult to
identify the [M]+ ion if you do not already know the structure of the compound. In any
event, you must try to find the [M]+ ion in the MS data first. The rest of MS
characterization depends upon this first step.

In the easiest cases, the [M]+ ion is the largest (highest/most intense) peak at the highest
m/z value. Not the highest peak, but the highest peak at the highest m/z. It is important to
remember that the [M]+ ion does not have to be the most intense ion, but it should be the
most intense signal (highest line) in the cluster of peaks at the highest m/z values.

The differing intensities of cations detected by the mass spectrometer are proportional to
the relative stabilities of the cations. Really stable cations show up as really large peaks,
unstable cations are either very small peaks or they do not show up at all. About 15% of
the time, the [M]+ is not seen because it is not stable enough. At other times, the [M]+ is
seen, but there are contamination peaks with higher m/z values that are also seen.
Contamination peaks indicate a dirty MS, not a dirty sample. You have to learn by
experience what the contaminant peaks in a MS from a particular instrument to expect.

While examining peaks in a MS data set, you will notice that one peak is always larger
(more intense/higher) than the others. The largest peak is significant, and we will learn
about it later. For the time being, it is enough to know that there is a largest peak in any
MS and that this most intense peak is called the base peak. It is also very important to
remember that the molecular ion (also called a parent ion) may or may not be the base
peak. All peaks with a lower value for m/z than the parent ion, [M]+, are smaller charged
cations (known as fragment or daughter ions) that have mass/charge values less than the
mass/charge value of the molecular ion. The fragment ions are made by loss of atoms
from the molecular ion. The types of peaks that may be present in a mass spectrum are
listed in Table III-2, on the next page. We will learn about fragmentation processes and
how they occur in later lessons.
 Base Peak The most intense peak in a MS spectrum.

Parent Peak
The molecular ion peak in a MS spectrum.

Peaks formed by the fragmentation of the

parent peak that have m/z values less than
Fragment Peaks that of the parent ion but which might have
a greater intensity than the parent ion has.

Table III-2. Terms for Ion Peaks That Must Be Memorized. MBM

At this point you will be expected to know that a MS spectrum definitely has a base peak,
it will also have fragment ions, and hopefully it will also have a parent (molecular) ion.
You are also expected to know how to predict a reasonable Lewis structure of a [M]+ for
a known compound. You should also be able to calculate the m/z value of a [M]+ of a
known structure. Now, you must learn how to perform the first step in analysis of MS
spectral data, finding the [M]+ ion. If present, it will be the largest peak in the cluster
of peaks with the greatest m/z values.

Q17. What are the values of m/z for the [M]+

and the base peak in the following tabulated MS
data?

m/z abundance
108 0.20
107 9.20
106 100
105 56
93 35
43 87
Q18. What are the values of m/z for the [M]+ A17.
and the base peak in the following tabulated MS
data? [M]+ = 106 m/z.
Base peak = 106 m/z
m/z abundance
176 11,124 The peak at 106 has the highest intensity of the
175 194,202 peaks with the largest m/z values (from 105 to
134 16,213 108) in this data set. The peak at m/z of 106
91 2,000,194 also happens to be the peak of greatest intensity
77 500,950 in the entire data set.
65 154,234

Q19. What are the values of m/z for the [M]+ A18.
and the base peak in the following tabulated MS
data? [M]+ = 175.
Base peak = 91
m/z abundance The molecular ion is the largest of the high m/z
97 1.1 peaks (175 & 176). The base peak is the largest
96 98.9 signal detected, in this case at a m/z of 91. The
95 1.1 abundance values are unitless. If normalized to
94 100 the abundance of the largest peak, the values
93 80 would range from 100 (for the largest) to 0.56
81 45 for the smallest peak at m/z of 176.
79 46 (11,124/2,000,194)*100 = 0.56
15 50

A19.

m/e of [M]+ = 94
m/e of base peak = 94
The molecular ion and base peak are the same in
this example. The peculiar feature of this data
set is the appearance of a nearly equal intensity
peak in the high m/z ion range (at 96). There is
a very rational explanation for this, which we
will cover in a future MS lesson. For now, just
remember to look at the peaks with the highest
m/z values and focus in on the most intense of
them as the likely [M]+ signal.