File Formats Commonly Used in Mass Spectrometry Proteomics

Automated Selected Reaction Monitoring Software for Accurate Label-Free Protein Quantification

(2012) Johan Teleman et al.   JOURNAL OF PROTEOME RESEARCH

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

(2012) Johannes Griss et al.   PROTEOMICS

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

(2011) Mi-Youn K Brusniak et al.   BMC BIOINFORMATICS

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

(2011) Harald Barsnes et al.   BMC BIOINFORMATICS

jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions

(2011) Kenny Helsens et al.   JOURNAL OF PROTEOME RESEARCH

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Comprehensive proteomics

(2010) Martin Beck et al.   CURRENT OPINION IN BIOTECHNOLOGY

ProHits: integrated software for mass spectrometry–based interaction proteomics

(2010) Guomin Liu et al.   NATURE BIOTECHNOLOGY

Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea

(2010) Sandra Orchard et al.   PROTEOMICS

The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

(2010) Frank Gibson et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

multiplierz: an extensible API based desktop environment for proteomics data analysis

(2009) Jignesh R Parikh et al.   BMC BIOINFORMATICS

Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry

(2009) S. E. Abbatiello et al.   CLINICAL CHEMISTRY

The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data

(2009) Jari Häkkinen et al.   JOURNAL OF PROTEOME RESEARCH

PRIDE Converter: making proteomics data-sharing easy

(2009) Harald Barsnes et al.   NATURE BIOTECHNOLOGY

mzAPI: a new strategy for efficiently sharing mass spectrometry data

(2009) Manor Askenazi et al.   NATURE METHODS

Managing the Data Explosion A Report on the HUPO-PSI Workshop August 2008, Amsterdam, The Netherlands

(2009) Sandra Orchard 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

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

(2008) Mi-Youn Brusniak et al.   BMC BIOINFORMATICS

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

(2008) Eric W Deutsch et al.   EMBO REPORTS

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

Thou shalt share your data

(2008)   NATURE METHODS

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

(2008) Eric W. Deutsch et al.   PHYSIOLOGICAL GENOMICS

mzML: A single, unifying data format for mass spectrometer output

(2008) Eric Deutsch   PROTEOMICS