David Tabb
Faculty Member
Last active: 6/26/2014

Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.

Holman JD, Ma ZQ, Tabb DL
Curr Protoc Bioinformatics. 2012 Chapter 13: Unit13.17

PMID: 22389012 · PMCID: PMC4547833 · DOI:10.1002/0471250953.bi1317s37

The identification of peptides and proteins by LC-MS/MS requires the use of bioinformatics. Tools developed in the Tabb Laboratory contribute significant flexibility and discrimination to this process. The Bumbershoot tools (MyriMatch, DirecTag, TagRecon, and Pepitome) enable the identification of peptides represented by MS/MS scans. All of these tools can work directly from instrument capture files of multiple vendors, such as Thermo RAW format, or from standard XML-based formats, such as mzML or mzXML. Peptide identifications are written to mzIdentML or pepXML format. Protein assembly is handled by the IDPicker algorithm. Raw identifications are filtered to a confident set by use of the target-decoy strategy. IDPicker arranges large sets of input files into a hierarchy for reporting, and the software applies a parsimony algorithm to report the smallest possible number of proteins to explain the observed peptides. This protocol details the use of these tools for new users.

MeSH Terms (7)

Algorithms Chromatography, Liquid Databases, Protein Mass Spectrometry Proteins Proteome Software

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