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MScDB: A Mass Spectrometry Centric Protein Sequence Database for Proteomics.
MedLine Citation:
PMID:  23627461     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Protein sequence databases are indispensable tools for life science research including mass spectrometry (MS)-based proteomics. In current database construction processes, sequence similarity clustering is used to reduce redundancies in the source data. Albeit powerful, it ignores the peptide centric nature of proteomic data and the fact that MS is able to distinguish similar sequences. Therefore, we introduce an approach that structures the protein sequence space at the peptide level using theoretical and empirical information from large-scale proteomic data to generate a mass spectrometry centric protein sequence database (MScDB). The core modules of MScDB are an in-silico proteolytic digest and a peptide centric clustering algorithm that groups protein sequences that are indistinguishable by mass spectrometry. Analysis of various MScDB use cases against five complex human proteomes, results in 69 peptide identifications not present in UniProtKB as well as 79 putative single amino acid polymorphisms. MScDB retains ~99% of the identifications in comparison to common databases despite a 3 - 48% increase in the theoretical peptide search space (but comparable protein sequence space). In addition MScDB enables cross-species applications such as human/mouse graft models and our results suggest that the uncertainty in protein assignments to one species can be smaller than 20%.
Authors:
Harald Marx; Simone Lemeer; Susan Klaeger; Thomas Rattei; Bernhard Kuster
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-4-30
Journal Detail:
Title:  Journal of proteome research     Volume:  -     ISSN:  1535-3907     ISO Abbreviation:  J. Proteome Res.     Publication Date:  2013 Apr 
Date Detail:
Created Date:  2013-4-30     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101128775     Medline TA:  J Proteome Res     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
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