In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types

Mass spectrometric analyses of protein digests produce large numbers of fragmentation spectra that are not identified by routine database searching strategies. Some of these spectra could be identified by development of improved search engines. However, many of these spectra represent fragmentation...

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Bibliographic Details
Published in:Molecular & cellular proteomics 2008-12, Vol.7 (12), p.2386-2398
Main Authors: Chalkley, Robert J., Baker, Peter R., Medzihradszky, Katalin F., Lynn, Aenoch J., Burlingame, A.L.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Databases, Protein
False Positive Reactions
Molecular Sequence Data
Molecular Weight
Peptides - analysis
Peptides - chemistry
ROC Curve
Software
Tandem Mass Spectrometry - instrumentation
Tandem Mass Spectrometry - statistics & numerical data
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Summary:Mass spectrometric analyses of protein digests produce large numbers of fragmentation spectra that are not identified by routine database searching strategies. Some of these spectra could be identified by development of improved search engines. However, many of these spectra represent fragmentation of peptide components bearing modifications that are not routinely considered in database searches. Here we present new software within Protein Prospector that allows comprehensive analysis of data sets by analyzing the data at increasing levels of depth. Analysis of published data sets is presented to illustrate that the software is not biased to any instrument types. The results show that these data sets contain many modified peptides. As well as searching for known modification types, Protein Prospector permits the detection and identification of unexpected or novel modifications by searching for any mass shift within a user-specified mass range to any chosen amino acid(s). Several modifications never previously reported in proteomics data were identified in these standard data sets using this mass modification searching approach.
ISSN:1535-9476
1535-9484
DOI:10.1074/mcp.M800021-MCP200