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

We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com. TraML files can also be converted online at http://iomics.ugent.be/jtraml.

[1]  R. Cooks,et al.  Multiple reaction monitoring in mass spectrometry/mass spectrometry for direct analysis of complex mixtures , 1978 .

[2]  Lennart Martens,et al.  PRIDE: The proteomics identifications database , 2005, Proteomics.

[3]  Pierre Marquet,et al.  LC-MS/MS systematic toxicological analysis: comparison of MS/MS spectra obtained with different instruments and settings. , 2005, Clinical biochemistry.

[4]  Eric W. Deutsch,et al.  The PeptideAtlas project , 2005, Nucleic Acids Res..

[5]  Leigh Anderson,et al.  Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins* , 2006, Molecular & Cellular Proteomics.

[6]  R. Aebersold,et al.  High Sensitivity Detection of Plasma Proteins by Multiple Reaction Monitoring of N-Glycosites*S , 2007, Molecular & Cellular Proteomics.

[7]  Henry H. N. Lam,et al.  A database of mass spectrometric assays for the yeast proteome , 2008, Nature Methods.

[8]  R. Aebersold,et al.  Selected reaction monitoring for quantitative proteomics: a tutorial , 2008, Molecular systems biology.

[9]  Lennart Martens,et al.  Analysis of the experimental detection of central nervous system‐related genes in human brain and cerebrospinal fluid datasets , 2008, Proteomics.

[10]  Christoph H Borchers,et al.  Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma* , 2009, Molecular & Cellular Proteomics.

[11]  Gennifer E. Merrihew,et al.  Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. , 2009, Journal of proteome research.

[12]  Lennart Martens,et al.  The PSI semantic validator: A framework to check MIAPE compliance of proteomics data , 2009, Proteomics.

[13]  John R Yates,et al.  Mass spectrometry in high-throughput proteomics: ready for the big time , 2010, Nature Methods.

[14]  Lennart Martens,et al.  The Ontology Lookup Service: bigger and better , 2010, Nucleic Acids Res..

[15]  Ruedi Aebersold,et al.  High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , 2010, Nature Methods.

[16]  Jingchun Chen,et al.  ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry , 2011, BMC Bioinformatics.

[17]  Lennart Martens,et al.  Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research , 2010, Journal of proteomics.

[18]  Lennart Martens,et al.  A global analysis of peptide fragmentation variability , 2011, Proteomics.

[19]  R. Aebersold,et al.  mProphet: automated data processing and statistical validation for large-scale SRM experiments , 2011, Nature Methods.

[20]  Lennart Martens,et al.  TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists* , 2011, Molecular & Cellular Proteomics.