UNIT 13.17 Identifying Proteomic LC-MS/MS Data Sets with Bumbershoot and IDPicker

  1. Jerry D. Holman,
  2. Ze-Qiang Ma,
  3. David L. Tabb

Published Online: 1 MAR 2012

DOI: 10.1002/0471250953.bi1317s37

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Holman, J. D., Ma, Z.-Q. and Tabb, D. L. 2012. Identifying Proteomic LC-MS/MS Data Sets with Bumbershoot and IDPicker. Current Protocols in Bioinformatics. 37:13.17:13.17.1–13.17.15.

Author Information

  1. Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee

Publication History

  1. Published Online: 1 MAR 2012
  2. Published Print: MAR 2012


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. Curr. Protoc. Bioinform. 37:13.17.1-13.17.15. © 2012 by John Wiley & Sons, Inc.


  • shotgun proteomics;
  • protein database search;
  • sequence tagging;
  • protein assembly;
  • proteome informatics;
  • peptide-spectrum matches