Analyzing Shotgun Proteomic Data with PatternLab for Proteomics
Open Access
- 1 June 2010
- journal article
- unit
- Published by Wiley in Current Protocols in Bioinformatics
- Vol. 30 (1), 13.13.1-13.13.15
- https://doi.org/10.1002/0471250953.bi1313s30
Abstract
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.Keywords
This publication has 13 references indexed in Scilit:
- GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics dataProteome Science, 2009
- PatternLab for proteomics: a tool for differential shotgun proteomicsBMC Bioinformatics, 2008
- A quantitative analysis software tool for mass spectrometry–based proteomicsNature Methods, 2008
- Validation of Tandem Mass Spectrometry Database Search Results Using DTASelectCurrent Protocols in Bioinformatics, 2006
- A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun ProteomicsAnalytical Chemistry, 2004
- Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression ProteomicsMolecular & Cellular Proteomics, 2002
- Gene Ontology: tool for the unification of biologyNature Genetics, 2000
- Probability-based protein identification by searching sequence databases using mass spectrometry dataElectrophoresis, 1999
- An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseJournal of the American Society for Mass Spectrometry, 1994