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

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).

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)

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 mass 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).

 

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. “Mass Spectral and GC Data of Drugs, Poisons, Pesticides, Pollutants and their Metabolites”, 2^ndEdition, VCH, 1992 
4. H.M. McNair, J.M. Miller, “Basic Gas Chromatography”, John Wiley &Sons, 1997 
5. M. Hamming and N. Foster. “Interpretation of Mass 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.