title: Pride-asap: automatic fragment ion annotation of identified PRIDE spectra.
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.
authors.affiliation: Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Niels
authors.initials: N
authors.lastname: Hulstaert
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Jonathan
authors.initials: J
authors.lastname: Rameseder
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D030562:Databases, Protein; D020407:Internet; D007477:Ions / Q000737:chemistry*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods* / Q000592:standards; D012984:Software
chemical_list: D007477:Ions
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