PatternLab: from mass spectra to label-free differential shotgun proteomics.

PatternLab: from mass spectra to label-free differential shotgun proteomics. Curr Protoc Bioinformatics. 2012 Dec;Chapter 13:Unit13.19 Authors: Carvalho PC, Fischer JS, Xu T, Yates JR, Barbosa VC Abstract PatternLab for proteomics is a self-contained computational environment for analyzing shotgun proteomic data. Recent improvements incorporate modules to facilitate the computational analysis, such as FastaDBXtractor for sequence database preparation and ProLuCID runner for simplifying and managing the protein identification search engine; modules for pushing the limits on proteomics standards, such as SEPro, which relies on a semi-labeled decoy approach for increasing confidence in filtering and organizing peptide spectrum matches; and modules with novel features, such as SEProQ for enabling label-free quantitation by extracted ion chromatograms according to a distributed normalized ion abundance factor approach (dNIAF). Existing modules were also improved, such as the TFold module for pinpointing differentially expressed proteins. These new modules are integrated into the previously described arsenal of tools for further data analysis. Here we provide detailed instructions for operating and understanding them. PMID: 23255152 [PubMed - indexed for MEDLINE]
Source: Current Protocols in Bioinformatics - Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research