Introduction

SUMMARY: Statistical validation of peptide assignments from a large-scale shotgun proteomics experiment is a critical step, and various methods for evaluating significance based on decoy database search are in practice. False discovery rate (FDR) estimation of peptide assignments assesses global significance and corrects for multiple comparisons. Various approaches have been proposed for FDR estimation but unavailability of standard tools or libraries leads to development of many in-house scripts followed by manual steps that are error-prone and low-throughput. The ProteoStats library provides an open-source framework for developers with many FDR estimation and visualization features for several popular search algorithms. It also provides accurate q-values, which can be easily integrated in any proteomics pipeline to provide automated, accurate, high-throughput statistical validation and minimize manual errors. AVAILABILITY: https://sourceforge.net/projects/mssuite/files/ProteoStats/. CONTACT: ddash@igib.res.in or aky.compbio@gmail.com or amit.yadav@igib.in. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. ProteoStats--a library for estimating false discovery rates in proteomics pipelines.
    Cite this
    Yadav AK, Kadimi PK, Kumar D, Dash D, 2013-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Amit Kumar Yadav
    Developer

    G.N.R. Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, India

  2. Puneet Kumar Kadimi
    Developer

  3. Dhirendra Kumar
    Developer

  4. Debasis Dash
    Investigator

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Summary
AccessionBT000132
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByDebasis Dash