ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer
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Date
2005-11
Publication Type
Journal Article
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yes
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Abstract
In MS/MS experiments with automated precursor ion, selection only a fraction of sequencing attempts lead to the successful identification of a peptide. A number of reasons may contribute to this situation. They include poor fragmentation of the selected precursor ion, the presence of modified residues in the peptide, mismatches with sequence databases, and frequently, the concurrent fragmentation of multiple precursors in the same CID attempt. Current database search engines are incapable of correctly assigning the sequences of multiple precursors to such spectra. We have developed a search engine, ProbIDtree, which can identify multiple peptides from a CID spectrum generated by the concurrent fragmentation of multiple precursor ions. This is achieved by iterative database searching in which the submitted spectra are generated by subtracting the fragment ions assigned to a tentatively matched peptide from the acquired spectrum and in which each match is assigned a tentative probability score. Tentatively matched peptides are organized in a tree structure from which their adjusted probability scores are calculated and used to determine the correct identifications. The results using MALDI-TOF-TOF MS/MS data demonstrate that multiple peptides can be effectively identified simultaneously with high confidence using ProbIDtree.
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published
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Journal / series
Volume
5 (16)
Pages / Article No.
4096 - 4106
Publisher
Wiley
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Methods
Software
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Subject
CID; MALDI-TOF; Multiple precursors; Peptide identification; Statistical analysis
Organisational unit
03663 - Aebersold, Rudolf (emeritus) / Aebersold, Rudolf (emeritus)