UNIT 13.13 Analyzing Shotgun Proteomic Data with PatternLab for Proteomics

  1. Paulo C. Carvalho1,2,
  2. John R. Yates III2,
  3. Valmir C. Barbosa1

Published Online: 1 JUN 2010

DOI: 10.1002/0471250953.bi1313s30

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Carvalho, P. C., Yates III, J. R. and Barbosa, V. C. 2010. Analyzing Shotgun Proteomic Data with PatternLab for Proteomics. Current Protocols in Bioinformatics. 30:13.13:13.13.1–13.13.15.

Author Information

  1. 1

    Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil

  2. 2

    The Scripps Research Institute, La Jolla, California

Publication History

  1. Published Online: 1 JUN 2010
  2. Published Print: JUN 2010


PatternLab for proteomics is a one-stop shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins/peptides that are differentially expressed and those that are unique to a state. It can also cluster the ones that share similar expression profiles in time-course experiments, as well as help in interpreting results according to Gene Ontology. PatternLab is user-friendly, simple, and provides a graphical user interface. Curr. Protoc. Bioinform. 30:13.13.1-13.13.15. © 2010 by John Wiley & Sons, Inc.


  • shotgun proteomics;
  • label-free proteomic analysis;
  • label-based proteomic analysis