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Interpreting Mass Spectra / GC–MS Data Analysis



GC-MS combines the advantages of both techniques the high resolving power and the speed of analysis of GC with the qualitative and quantitative analytical capabilities of the MS down to the ppb level. Mass ranges of 10 to 1000 Daltons are common to GC-MS systems today.

A typical G.C.chromatogram of a mixture run on GC-MS has the same appearance as it would with an FID (see Fig. 1).

Fig. 1: Total ion chromatogram of a mixture
Fig. 1: Total ion chromatogram of a mixture


Let’s suppose that the first peak in the above chromatogram is the peak of hexane. The mass spectrum of hexane is shown on Fig. 2.

 
Fig. 2: Mass spectrum of n-hexane (EI).
Fig. 2: Mass spectrum of n-hexane (EI).
A proposed mechanism for the fragmentation of n-hexane in the ion source of a GC-MS system is presented below (Fig. 3):
  • An electron strikes the parent molecule, ejecting one electron and generating the molecular ion (m/z=86).
  • This species is not stable, however, and rapidly decomposes to more stable fragments in this case  m/z  of 71, 57, 43 and 29 Daltons.
  • The fragment with the highest abundance m/z = 57 is called the base peak and is plotted to 100% of the spectrum scale.



Fig. 3: Fragmentation of hexane in a mass spectrometer (EI)
Fig. 3: Fragmentation of hexane in a mass spectrometer (EI)


Straight chain alkanes and alkyl groups produce a typical series of peaks: 29 (CH3CH2+), 43 (CH3CH2CH2+), 57 (CH3CH2CH2CH2+), 71 (CH3CH2CH2CH2CH2+) etc.

Some of the most common fragments in mass spectrometry are given in the table below. Complete lists of common fragments can be obtained from the references listed below.

Table 1: List of common fragments in mas s spectra

Fragments
m/z
Fragments
m/z
CH2
14
NO2
46
CH3
15
CH2SH
47
O
16
CH3S + H
48
OH
17
CH2Cl
49
H2O, NH4
18
CHF2, C3H3
51
F
19
C4H5
53
CN, C2H2
26
CH2CH2CN
54
C2H3
27
C4H7
55
C2H4, CO
28
C4H8
56
C2H5, CHO
29
C4H9, C2H5C=O
57
CH2NH2
30
CH3C(=O)CH2 + H
C2H5CHNH2
58
CH2OH
31
C3H6OH, CH2OC2H5
59
O2
32
CH2COOH
60
SH
33
CH3COO
61
H2S
34
C5H5
65
Cl
35
C5H6
66
HCl
36
C5H7
67
C3H3
39
CH2CH2CH2CN
68
C3H5
41
C5H9, CF3
69
C3H6, C2H2O
42
C5H10
70
C3H7, CH3C=O
43
C5H11
71
CH2CHO
44
C6H4
76
CH3CHOH, CH2CH2OH, CH2OCH2
45
C6H5
77

Let’s examine the case of 3-methyl hexane. The mass spectrum of the compound is shown in Fig. 4.

Fig. 4: Mass spectrum of 3-methyl-hexane (EI).

Fig. 4: Mass spectrum of 3-methyl-hexane (EI).
 
The parent ion M+ at m/z = 100 is too weak but it can be seen.
M – CH3  →  m/z = 85
M – CH2CH3   →  m/z = 71
M – CH2CH2CH3   →  m/z = 57

M – CH2CH2CH2CH3   →  m/z = 43   ( the Base Peak, the most abundant)

CH3CH2CH2CH   →    m/z = 56



REFERENCES


  1. D. Harvey,  “Modern Analytical Chemistry”, McGraw-Hill Companies Inc., 2000 
  2. J. Willett , “Gas Chromatography”, John Wiley &Sons, 1987 
  3. K. Pfleger et al. “Mas s Spectral and GC Data of Drugs, Poisons, Pesticides, Pollutants and their Metabolites”, 2nd Edition, VCH, 1992 
  4. H.M. McNair, J.M. Miller, “Basic Gas Chromatography”, John Wiley &Sons, 1997 
  5. M. Hamming and N. Foster. “Interpretation of Mas s Spectra of Organic Compounds”. New York, NY. Academic Press                                                                                        
  6. F.W. McLafferty, “Interpretation of Mass Spectra” Mill Valley, CA. University Scientific Books 
  7. R.G. Silverstein et al., “Spectrometric Identification of Organic Compounds” New York, NY. John Wiley and Sons. Inc.





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