On the relevance of peptide sequence permutations in shotgun proteomics studies

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 ∼25% in the higher-confidence data set, compared to an estimated incidence of false positives for permuted masses (maximum ∼8%), based on a null-hypothesis decoy data set.