Protein Identification with Tandem Mass Spectrometry Data

Abstract

There are two ways to identify proteins from peptide MS-MS spectra. The first is de novo interpretation of the spectrum to obtain a peptide sequence followed by BLAST searching of the sequence against a sequence database to identify the protein. This is a perfectly reasonable approach—as long as there are only a few spectra to deal with. Manual de novo interpretation of an individual MS-MS spectrum takes between half an hour and a couple of days, depending on the complexity of the spectrum and the experience of the analyst. As noted earlier, some spectra do not contain complete b- or y-ion series and thus it may not be possible to unambiguously interpret a peptide sequence from these spectra. The analyst then must guess at sequence where the spectral clues fall short. Of course, accurate de novo interpretation of MS-MS spectra requires skill and experience. Nevertheless, we could easily use this approach to assign the sequences of several peptides in a sample and identify the precursor protein by BLAST searching within a day or two. This could be perfectly acceptable, for example, to identify one or two proteins from bands on an SDS gel.