GAPP: A fully automated software for the confident identification of human peptides from tandem mass spectra

Ian Shadforth, Weibing Xu, Daniel Crowther, Conrad Bessant

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

This paper introduces the genome annotating proteomic pipeline (GAPP), a totally automated publicly available software pipeline for the identification of peptides and proteins from human proteomic tandem mass spectrometry data. The pipeline takes as its input a series of MS/MS peak lists from a given experimental sample and produces a series of database entries corresponding to the peptides observed within the sample, along with related confidence scores. The pipeline is capable of finding any peptides expected, including those that cross intron-exon boundaries, and those due to single nucleotide polymorphisms (SNPs), alternate splicing, and post-translational modifications (PTMs). GAPP can therefore be used to re-annotate genomes, and this is supported through the inclusion of a Distributed Annotation System (DAS) server, which allows the peptides identified by the pipeline to be displayed in their genomic context within the Ensembl genome browser. GAPP is freely available via the web, at www.gapp.info.

Original languageEnglish
Pages (from-to)2849-2852
Number of pages4
JournalJournal of Proteome Research
Volume5
Issue number10
DOIs
Publication statusPublished - 16 Aug 2006

Keywords

  • Bioinformatics
  • Grid
  • High throughput
  • Mass spectrometry
  • Proteomics

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