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jmzML specifications

Information


Unique identifier OMICS_03340
Name jmzML
Software type Framework/Library, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Version 1.6.7
Stability Stable
Maintained Yes

Subtool


  • mzML Viewer Application

Versioning


No version available

Documentation


Maintainer


  • person_outline Lennart Martens

Additional information


https://code.google.com/archive/p/jmzml/wikis

Publication for jmzML

jmzML citations

 (8)
library_books

Fast and Efficient XML Data Access for Next Generation Mass Spectrometry

2015
PLoS One
PMCID: 4416046
PMID: 25927999
DOI: 10.1371/journal.pone.0125108

[…] support for multiple standard formats. Some of the more popular tools that strive towards standard-compliant implementation of (one or more) PSI formats are the ProteoWizard library [, ], mspire [], jmzML [] mzR [], the PRIDE toolsuite [], jmzReader [] and the OpenMS library [] (see also Perez-Riverol et al. [] for a recent discussion of different open source software libraries in mass spectromet […]

library_books

Development of data representation standards by the human proteome organization proteomics standards initiative

2015
PMCID: 4457114
PMID: 25726569
DOI: 10.1093/jamia/ocv001

[…] ssential to promote adoption and to provide developers to include support for the standards in tools. These software libraries provide reading/writing functionality and other extra features. They are jmzML, jTraml, jmzIdentML, jmzQuantML, mzidLibrary, and jmzTab. Many open-source software tools implement the standards. Some of them were developed in Java making use of these libraries, but other pr […]

library_books

Universal database search tool for proteomics

2014
Nat Commun
PMCID: 5036525
PMID: 25358478
DOI: 10.1038/ncomms6277

[…] GF+ takes a spectral dataset Spectra and a protein database ProteinDB as an input and outputs a set of scored PSMs along with E-value estimates. It uses open source application programming interfaces jmzML [], jmzReader [], and jmzIdentML [], and supports the HUPO Proteomics Standard Initiative standard file formats – mzML [] and mzIdentML []. Due to these developments, MS-GF+ has been already ado […]

library_books

A tutorial for software development in quantitative proteomics using PSI standard formats☆

2014
Biochim Biophys Acta
PMCID: 4008935
PMID: 23584085
DOI: 10.1016/j.bbapap.2013.04.004

[…] ch are mandatory. Both can act as a unique identifier for the spectrum; however, we recommend that developers use the id element as the primary unique identifier for a spectrum, especially when using jmzML (see below), since some file manipulations could alter the index attribute but the id value should never change. The different attributes (e.g. MS level for each scan) are specified in the CV pa […]

library_books

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice☆

2014
Biochim Biophys Acta
PMCID: 3898906
PMID: 23429179
DOI: 10.1016/j.bbapap.2013.02.017

[…] d formats developed by the HUPO-PSI working group, which developed several Java libraries for the memory-efficient reading and writing of the information contained in the respective standard formats: jmzML , jTraML , jmzIdentML , jmzReader and jmzQuantML . The mzML format is the successor of the merged formats mzData and mzXML . In addition, the alternative de facto standard formats pepXML and […]

library_books

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

2014
Biochim Biophys Acta
PMCID: 3898926
PMID: 23467006
DOI: 10.1016/j.bbapap.2013.02.032

[…] ore, the PRIDE toolsuite also contains several Java APIs for read/write several standard formats, some of which are used in PRIDE Converter 2 and PRIDE Inspector, but also in other external software: jmzML for mzML, jmzIdentML for mzIdentML, and the new jmzTab (http://mztab.googlecode.com) to read and write mzTab files. Both jmzML and jmzIdentML use the XXindex library (http://pride-toolsuite.go […]

Citations

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jmzML institution(s)
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
jmzML funding source(s)
Supported by the "ProDaC" grant LSHGCT-2006-036814 of the European Union.

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