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

J Proteomics. 2013 Dec 16;95(100):89-92. doi: 10.1016/j.jprot.2013.04.011. Epub 2013 Apr 17.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein*
  • Internet*
  • Ions / chemistry*
  • Proteomics / instrumentation
  • Proteomics / methods*
  • Proteomics / standards
  • Software*

Substances

  • Ions