Mass spectrometry peptide assignment

Presently, FAB-MS spectra are routinely used to characterize synthetic tyrosine O-sulfate peptides.152,57,63-671 Since partial hydrolysis of the sulfate ester occurs in the gas phase, quantification of the tyrosine O-sulfate residue by mass spectrometry is not possible, but combined with one-peak assignment in HPLC, FAB-MS represents a powerful analytical tool. On the other hand, partial hydrolysis in the gas phase excludes the presence of sul-fonated species which should be perfectly stable. In early studies the presence of such species were excluded by quantitative recovery of tyrosine upon acid hydrolysis or upon hydrolysis with arylsulfatase.1361 Recently, even MALDI-TOF-MS spectra of CCK-peptides1441 and of conotoxins a-PnIA and a-PnlB 138 were reported which show that in the positive-ion mode the [M + H-S03]+ ions represent the base peaks, while in the negative-ion mode, [M-H]-ions consistently correspond to the base peaks. In the CCK peptides intramolecular salt bridging of the sulfate hemi-ester with proximal positive charges of arginine or lysine side chains was found to reduce the extent of hydrolysis in the gas phase significantly.144,1491... 

Tryptic Maps of Relaxin and Relaxin B-chain. Digestion of the A-chain of human relaxin with trypsin can theoretically result in the release of five fragments that of the B-chain in the release of six fragments as illustrated in Table II. A typical tryptic map of relaxin B-chain is shown in Figure 2. The peptide was reduced and carboxymethylated with iodoacetic acid before enzymatic digestion. The peptide assignments were made after analysis of the peaks by amino acid hydrolysis for amino acid composition and confirmed by fast atom bombardment mass spectrometry (FAB-MS) as shown in Table IH... 

We have implemented scanning methodologies using MALDI-TOF mass spectrometry to partially purified venom from C. striatus and C. ermineus. We have carried out specific derivatizations in order to deduce composition and sequence information. Together with an intact mass these measurements are used to determine whether an ionized species observed in the MALDI mass spectrum corresponds with the intact protonated molecule of a previously characterized conotoxin. The information obtained from derivatizations is also important when the ionized species does not correspond with the intact mass of peptides of known sequence. In that case, post source decay of the native and derivatized species may help assign the fragment ions. 

While those who used the MALDI-TOF MS data had a higher accuracy of positive assignments, this study indicated there are many respondents who are not well versed in the proper use of mass spectrometry data. Respondents can use mass spectra data to confirm sequence assignments within approximately 0.1% accuracy of the measured mass, to estimate the length of a peptide, and to potentially confirm tentative amino acids. The mass spectral data should not be used to estimate the ratios of ions present. The web sites listed in Table II provide a ready resource to aid in this process. 

Finally, disulphide bonds can be located by hydrolysing a protein to a mixture of peptides using either a proteinase or a specific chemical method of cleavage and the mixture can be analysed directly by fast-atom bombardment mass spectrometry (Chapter 3) and again after reduction of disulphide bonds (Yazdanparast et al., 1987). By identifying those peaks which disappear as a result of reduction and new peaks with appropriate masses that have taken their place, it is simple to assign disulphide bonds to the relevant amino-acid sequences. 

Neutral Loss-Driven ECD Represents a method when ECD in the FTICR unit of the instrument is initiated on precursor ions of peptides showing the specified NL in the MS/MS scan acquired via collision-induced dissociation-tandem mass spectrometry (CID-MS/MS) in the linear ion trap. ECD helps in correct assignment of sites of modification when more than one candidate site is present, because this method of peptide dissociation tends to retain the modifying group during MS/MS of the precursor ion. 

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