Mining a Tandem Mass Spectrometry Database To Determine the Trends and Global Factors Influencing Peptide Fragmentation

详细信息    查看全文

• 作者：Eugene A. Kapp ; Fré ; dé ; ric Schü ; tz ; Gavin E. Reid ; James S. Eddes ; Robert L. Moritz ; Richard A. J. O'Hair ; Terence P. Speed ; and Richard J. Simpson
• 刊名：Analytical Chemistry
• 出版年：2003
• 出版时间：November 15, 2003
• 年：2003
• 卷：75
• 期：22
• 页码：6251 - 6264
• 全文大小：416K
• 年卷期：v.75,no.22(November 15, 2003)
• ISSN：1520-6882

文摘

A database of 5500 unique peptide tandem mass spectraacquired in an ion trap mass spectrometer was assembledfor peptides derived from proteins digested with trypsin.Peptides were identified initially from their tandem massspectra by the SEQUEST algorithm and subsequentlyvalidated manually. Two different statistical methods wereused to identify sequence-dependent fragmentation patterns that could be used to improve fragmentation modelsincorporated into current peptide sequencing and database search algorithms. The currently accepted "mobileproton" model was expanded to derive a new classificationscheme for peptide mass spectra, the "relative protonmobility" scale, which considers peptide ion charge stateand amino acid composition to categorize peptide massspectra into peptide ions containing "nonmobile", "partially mobile", or "mobile" protons. Quantitation of amidebond fragmentation, both N- and C-terminal to any givenamino acid, as well as the positional effect of an aminoacid in a peptide and peptide length on such fragmentation, has been determined. Peptide bond cleavage propensities, both positive (i.e., enhanced) and negative (i.e.,suppressed), were determined and ranked in order oftheir cleavage preferences as primary, secondary, ortertiary cleavage effects. For example, primary positivecleavage effects were observed for Xaa-Pro and Asp-Xaabond cleavage for mobile and nonmobile peptide ioncategories, respectively. We also report specific pairwiseinteractions (e.g., Asn-Gly) that result in enhanced amidebond cleavages analogous to those observed in solution-phase chemistry. Peptides classified as nonmobile gavelow or insignificant scores, below reported MS/MS scorethresholds (cutoff filters), indicating that incorporation ofthe relative proton mobility scale classification would leadto improvements in current MS/MS scoring functions.