Fragment ion peaks

Tabb, D. L. Huang, Y. Wysocki, V. H. Yates, J. R. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 2004, 76,1243-1248. 

Often but not necessarily, the peak at highest m/z results from the detection of the intact ionized molecule, the molecular ion, M. The molecular ion peak is usually accompanied by several peaks at lower m/z caused by fragmentation of the molecular ion to yield fragment ions. Consequently, the respective peaks in the mass spectrum may be referred to as fragment ion peaks. 

Example In the electron ionization mass spectmm of a hydrocarbon, the molecular ion peak and the base peak of the spectrum correspond to the same ionic species at m/z 16 (Fig. 1.2). The fragment ion peaks at m/z 12-15 are spaced at 1 u distance. Obviously, the molecular ion, M" , fragments by loss of H which is the only possibility to explain the peak at m/z 15 by loss of a neutral of 1 u mass. Accordingly, the peaks at lower m/z might arise from loss of a H2 molecule (2 u) and so forth. It does not take an expert to recognize that this spectrum belongs to methane, CH4, showing its molecular ion peak at m/z 16 because the atomic mass... 

Although convenient at first sight, the lack of fragment ion peaks in FI spectra also means a lack of structural information. If more than an estimate of the elemental composition based on the isotopic pattern is desired, collision-induced dissociation (CID, Chap. 2.12.1) can deliver fragment ions for structure elucidation. Fortunately, the fragmentation pathways of IVT ions in CID are the same as in EI-MS (Chap. 6). 

There is theoretical interest in thietene because if it were to lose hydride ion a potentially aromatic cation having An + 1 electrons, where = 0, might form (Scheme 8.16). Intriguingly, the mass spectrum of thietene, molecular mass 72, shows a fragment ion peak at mh 71 ... 

The presence of an M - 15 peak (loss of CH3), or an M - 18 peak (loss of H20), or an M — 31 peak (loss of OCH3 from methyl esters), and so on, is taken as confirmation of a molecular ion peak. An M — 1 peak is common, and occasionally an M - 2 peak (loss of H2 by either fragmentation or thermolysis), or even a rare M - 3 peak (from alcohols) is reasonable. Peaks in the range of M - 3 to M — 14, however, indicate that contaminants may be present or that the presumed molecular ion peak is actually a fragment ion peak. Losses of fragments of masses 19-25 are also unlikely (except for loss of F = 19 or HF = 20 from fluorinated compounds). Loss of 16 (O), 17 (OH), or 18 (H20) are likely only if an oxygen atom is in the molecule. 

A third indication that an ion is indeed the molecular ion may be obtained from an examination of the fragment ion peaks in the vicinity of the ion. Mass losses of between 3 and 15 and between 20 and 26 are highly unlikely, and if they are observed would suggest that the putative molecular ion is in fact a fragment ion. 

NO, NO2, and O2 in some of the polyaromatic-polar fractions. Also, the El results for the -15N and -17N series are somewhat high, probably due to interference from fragment ion peaks. 

A slight difference between peaks C and D is observed in other fragment ion peaks such as m/e 51, 61, 63, 79, 80, 115, and 128. This comparison implies that these two intermediates have similar chemical structures. 

Identify all members of the b- or j-sequence ion-series. For this, it is helpful to identify the (n — l)th ion first and then by matching the mass difference between each of the fragment ion peaks with the residue masses, the amino acids present are then recognized. Only the residue masses of 20 naturally occurring amino acids are considered (Table 2). This procedure is used in Figure 13. 

Fig. 1.7. Scattering of Sbg clusters from an HOPG surface, (a) Integral yield of the ions scattered off the surface and (b) relative intensity of the observed major fragment ion peaks as a function of the cluster-surface collision energy [58,87]...

Mass spectral data are available for compounds 1 and 5-9 only an signal is reported for compound 1 [76ZAAC(423)47], while little fragmented ion peaks are observed in their El mass spectra for compounds 5-9. APCI mass spectral data of compounds 5,6,8 and 9 in MeCN with 1 % HCl exhibit a similar trend monocyclic bismuthenium cations provide predominant signals due to the cleavage of one Bi-S bond [96JA3225]. 

In the mass spectrum of both alkaloids and their dihydro-derivatives appears a fragment ion peak at mje 201 (a). In the spectrum of A-methylcinchophyllamine, obtained by lithium aluminium hydride reduction of the iV-formyl derivative, the peak is shifted to mje 215. 

The information to be gained from a mass spectrum is naturally dependent on structure. Serpentinine (253) gives an extremely complicated, worthless spectrum in which no molecular ion appears. The spectrum of C-curarine dichloride (54) shows only the molecular ion of the bisnor-base, while for calebassine dichloride (55) only the peaks corresponding to the loss of one and two molecules of water from the bisnor-base are observed. The other curare alkaloids also yield spectra which show a lack of fragment ion peaks they share this characteristic with strychnine. 

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