Open AccessUsing PSEA‐Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry‐Based Proteomics
Author(s) -
LavalléeAdam Mathieu,
Yates John R.
Publication year - 2016
Publication title -
current protocols in bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.535
H-Index - 57
eISSN - 1934-340X
pISSN - 1934-3396
DOI - 10.1002/0471250953.bi1328s53
Subject(s) - proteomics , mass spectrometry , troubleshooting , set (abstract data type) , chemistry , computational biology , computer science , chromatography , biology , gene , biochemistry , programming language , operating system
PSEA‐Quant analyzes quantitative mass spectrometry–based proteomics datasets to identify enrichments of annotations contained in repositories such as the Gene Ontology and Molecular Signature databases. It allows users to identify the annotations that are significantly enriched for reproducibly quantified high abundance proteins. PSEA‐Quant is available on the Web and as a command‐line tool. It is compatible with all label‐free and isotopic labeling‐based quantitative proteomics methods. This protocol describes how to use PSEA‐Quant and interpret its output. The importance of each parameter as well as troubleshooting approaches are also discussed. © 2016 by John Wiley & Sons, Inc.