obaDIA: one-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data.

Abstract

Data mining and data quality evaluation are indispensable constituents of quantitative proteomics, but few integrated tools available. We introduced obaDIA, a one-step pipeline to generate visualizable and comprehensive results for quantitative proteomics data. obaDIA supports fragment-level, peptide-level and protein-level abundance matrices from DIA technique, as well as protein-level abundance matrices from other quantitative proteomic techniques. The result contains abundance matrix statistics, differential expression analysis, protein functional annotation and enrichment analysis. Additionally, enrichment strategies which use total proteins or expressed proteins as background are optional, and HTML based interactive visualization for differentially expressed proteins in the KEGG pathway is offered, which helps biological significance mining. In short, obaDIA is an automatic tool for bioinformatics analysis for quantitative proteomics. obaDIA is freely available from https://github.com/yjthu/obaDIA.git. Supplementary data are available at Bioinformatics online.