Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

(2013) G. Mayer et al.   Database-The Journal of Biological Databases and Curation

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

(2012) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

(2012) Florian Reisinger et al.   PROTEOMICS

compomics-utilities: an open-source Java library for computational proteomics

(2011) Harald Barsnes et al.   BMC BIOINFORMATICS

Hierarchical Clustering of Shotgun Proteomics Data

(2011) Ville R. Koskinen et al.   MOLECULAR & CELLULAR PROTEOMICS

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results

(2010) Thilo Muth et al.   PROTEOMICS

Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies

(2010) Brian C. Searle   PROTEOMICS

MassSieve: Panning MS/MS peptide data for proteins

(2010) Douglas J. Slotta et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

OMSSA Parser: An open-source library to parse and extract data from OMSSA MS/MS search results

(2009) Harald Barsnes et al.   PROTEOMICS

The PSI semantic validator: A framework to check MIAPE compliance of proteomics data

(2009) Luisa Montecchi-Palazzi et al.   PROTEOMICS

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

The PSI-MOD community standard for representation of protein modification data

(2008) Luisa Montecchi-Palazzi et al.   NATURE BIOTECHNOLOGY

Guidelines for reporting the use of mass spectrometry informatics in proteomics

(2008) Pierre-Alain Binz et al.   NATURE BIOTECHNOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY