Protein Identification with Tandem Mass Spectrometry Data
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.
KeywordsPeptide Sequence Protein Identification Tandem Mass Spectrum Correct Match Rapid Assignment
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