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J Proteomics. 2013 Dec 16;95:89-92. doi: 10.1016/j.jprot.2013.04.011. Epub 2013 Apr 17.

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra.

Author information

1
Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium.

Abstract

We present an open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database. Pride-asap can be ran in a command line mode for automated processing of multiple PRIDE experiments, but also has a graphical user interface that allows end users to annotate the spectra in PRIDE experiments and to inspect the results in detail. Pride-asap binaries, source code and additional information can be downloaded from http://pride-asa-pipeline.googlecode.com.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.

KEYWORDS:

API; Automatic Spectrum Annotation Pipeline; Bioinformatics; GUI; Mass spectrometry; PRIDE; PRoteomics IDEntifications (database); PSM; PTM; Proteomics; application programming interface; asap; graphical user interface; peptide spectrum match; post-translational modification

PMID:
23603108
PMCID:
PMC4085470
DOI:
10.1016/j.jprot.2013.04.011
[Indexed for MEDLINE]
Free PMC Article
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