Protein Identification with Tandem Mass Spectrometry Data

  • Daniel C. Liebler


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.


Peptide Sequence Protein Identification Tandem Mass Spectrum Correct Match Rapid Assignment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Suggested Reading

  1. Clauser, K. R., Baker, P., and Burlingame, A. L. (1999) Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871–2882.PubMedCrossRefGoogle Scholar
  2. Yates, J. R., Eng, J. K., and McCormack, A. L. (1995) Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67, 3202–3210.PubMedCrossRefGoogle Scholar
  3. Yates, J. R., Eng, J. K., McCormack, A. L., and Schieltz, D. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426–1436.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2002

Authors and Affiliations

  • Daniel C. Liebler
    • 1
  1. 1.College of PharmacyThe University of ArizonaTucsonUSA

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