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Mass Mapping
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Protein Analytics - Mass Mapping

  • Most clients submit samples in SDS-PAGE gels, representing a single, well-resolved protein band.  In fact, seemingly well-resolved bands often contain two or more proteins, and we will often detect two to four proteins in a single sample.  Samples of greater complexity than this may generate a poor result.  We digest samples with trypsin and analyze them with a Sciex TOF/TOF 5800 MALDI mass spectrometer using a combination of MS and MS/MS modes.  We may employ a variety of search engines available on the internet; these programs perform a “best fit” mass analysis of both the peptide map (MS); and the fragmentation data (MS/MS), combined into a single searchable text file.  The data is compared with theoretical digests for all proteins that are archived in one of the public databases. In general we use “Mascot” for this purpose.

  • For each sample analyzed we return a Result Summary page on which the best match is listed at the top and alternative matches are given in descending order of probability score.  It should be stressed that mass mapping generates inferential evidence of protein identity, as opposed to empirical protein sequence data that is generated, for example, by Edman degradation. The programs we use to match mass spectrometric profiles provide putative peptide sequence data corresponding to peptides from the matching database protein.