jmzML, an open-source Java API for mzML, the PSI standard for MS data

Proteomics
Richard G CôtéLennart Martens

Abstract

We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.

References

Nov 6, 2004·Nature Biotechnology·Patrick G A PedrioliRuedi Aebersold
Jul 26, 2005·Proteomics·Lennart MartensRolf Apweiler
Mar 28, 2008·BMC Bioinformatics·Marc SturmOliver Kohlbacher
Jul 9, 2008·Bioinformatics·Darren KessnerParag Mallick
Oct 17, 2009·Proteomics·Luisa Montecchi-PalazziHenning Hermjakob

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Citations

Aug 19, 2010·Molecular & Cellular Proteomics : MCP·Lennart MartensEric W Deutsch
Jun 24, 2010·Omics : a Journal of Integrative Biology·Roger HigdonEugene Kolker
Mar 8, 2011·Omics : a Journal of Integrative Biology·Sam Hanash
Jul 19, 2012·Omics : a Journal of Integrative Biology·Faviel F Gonzalez-GalarzaAndrew R Jones
Dec 4, 2012·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Mar 10, 2011·BMC Bioinformatics·Harald BarsnesLennart Martens
Nov 2, 2014·Nature Communications·Sangtae Kim, Pavel A Pevzner
Nov 4, 2015·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Dec 1, 2012·Expert Review of Proteomics·Marc VaudelLennart Martens
Jul 5, 2015·Journal of Proteomics·Oliver HorlacherFrederique Lisacek
Jul 18, 2015·Journal of Proteomics·Gerhard MayerMartin Eisenacher
Jan 16, 2013·Proteomics·Alexander R IvanovSusan T Weintraub
Jan 16, 2013·Proteomics·J Alberto Medina-AunonAndrew J Jones
Mar 25, 2014·Proteomics·Qing-Wei XuJuan Antonio Vizcaíno
Feb 23, 2013·Biochimica Et Biophysica Acta·Gerhard MayerMartin Eisenacher
Apr 16, 2013·Biochimica Et Biophysica Acta·Faviel F Gonzalez-GalarzaAndrew R Jones
Mar 8, 2013·Biochimica Et Biophysica Acta·Yasset Perez-RiverolJuan Antonio Vizcaíno
May 1, 2015·PloS One·Hannes L RöstLars Malmström
Jun 7, 2014·Journal of Proteome Research·Wout BittremieuxKris Laukens
Mar 3, 2015·Journal of the American Medical Informatics Association : JAMIA·Eric W DeutschHenning Hermjakob
Mar 29, 2014·Molecular & Cellular Proteomics : MCP·Johan TelemanFredrik Levander
Mar 1, 2017·Methods of Information in Medicine·Stefan KropfKerstin Denecke
Nov 8, 2017·BMC Bioinformatics·Jebediah RosenRob Smith
Feb 6, 2018·Journal of Proteome Research·Andrew Collins, Andrew R Jones
Mar 21, 2018·Journal of Proteome Research·Salvador Martínez-BartoloméJuan Pablo Albar
Sep 10, 2020·Journal of Proteome Research·Laurent GattoJohannes Rainer
Dec 24, 2018·Journal of Proteome Research·Lev I LevitskyMikhail V Gorshkov

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