期刊
JOURNAL OF PROTEOME RESEARCH
卷 10, 期 5, 页码 2409-2416出版社
AMER CHEMICAL SOC
DOI: 10.1021/pr101235w
关键词
sequence scrambling; peptide size; collision-induced dissociation; tandem mass spectrometry
资金
- University of Florida
- National Science Foundation [CHE-0845450]
- American Society for Mass Spectrometry
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [0845450] Funding Source: National Science Foundation
In collision-induced dissociation (CID) of peptides, it has been observed that rearrangement processes can take place that appear to permute/scramble the original primary structure, which may in principle adversely affect peptide identification. Here, an analysis of sequence permutation in tandem mass spectra is presented for a previously published proteomics study on P. aeruginosa (Scherl et al., J. Am. Soc. Mass Spectrom. 2008, 19, 891) conducted using an LTQ-orbitrap. Overall, 4878 precursor ions are matched by considering the accurate mass (i.e., < 5 ppm) of the precursor ion and at least one fragment ion that confirms the sequence. The peptides are then grouped into higher- and lower-confidence data sets, using five fragment ions as a cutoff for higher-confidence identification. It is shown that the propensity for sequence permutation increases with the length of the tryptic peptide in both data sets. A higher charge state (i.e., 3+ vs 2+) also appears to correlate with a higher appearance of permuted masses for larger peptides. The ratio of these permuted sequence ions, compared to all tandem mass spectral peaks, reaches similar to 25% in the higher-confidence data set, compared to an estimated incidence of false positives for permuted masses (maximum similar to 8%), based on a null-hypothesis decoy data set.
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