mzQuantML specifications


Unique identifier OMICS_14624
Name mzQuantML
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 1.0.1
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Andrew Jones <>

Publication for mzQuantML

mzQuantML in publications

PMCID: 5500760
PMID: 28515314
DOI: 10.1074/mcp.M117.068429

[…] engines, the mzidentml format was released as a stable version (version 1.1) in the last quarter of 2011, and published in 2012 (). a separate format for quantitative results was built, called mzquantml—initially defined for large scale discovery approaches () and updated to also support targeted approaches, such as selected reaction monitoring (). more recently, in 2014, a lighter […]

PMCID: 5414595
PMID: 28118949
DOI: 10.1016/j.tibs.2017.01.001

[…] formats are: (i) mzml, which stores raw ms data as well as processed peak list spectra ; (ii) mzidentml, which captures the peptide and protein identifications derived from ms data ; and (iii) mzquantml, which captures detailed quantitative information . besides these three xml-based formats, a simpler, tab-delimited format called mztab has been released that stores both identification […]

PMCID: 4738454
PMID: 26449181
DOI: 10.1002/pmic.201500295

[…] resulted in key data standards for the field, including mzml (for ms data), mzidentml (for peptide/protein identification data), mztab (for peptide/protein identification and quantification data), mzquantml (for peptide/protein quantification data), and traml (for transition lists in targeted proteomics approaches) , , , , . importantly, support for these standards is provided through software […]

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mzQuantML institution(s)
Quantitative Biology Center and Department of Computer Science, Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Institute of Integrative Biology, University of Liverpool, Liverpool, UK; Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany; Bioinformatics Group, Cranfield Health, Cranfield University, Cranfield, UK; Institute for Systems Biology, Seattle, WA, USA; EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain
mzQuantML funding source(s)
The tool is funded by MedSys (BMBF grant number 0315450), the EU FP7 “ProteomeXchange” grant (grant number 260558), LipidomicNet (grant number 202272), PRIME-XS (grant number 262067) and MARINA (grant number 236215), CLIB (“Cluster Industrielle Biotechnologie”) within the QProM project (contract number 616 40003 0315413B), P.U.R.E. (Protein Unit for Research in Europe), a project of Nordrhein-Westfalen, a federal state of Germany, BBSRC (BB/I00095X/1, BB/H024654/1 and BB/I001131/1), NIGMS grant GM087221, NHGRI grant HG005805, the Systems Biology Initiative of the State of Luxembourg, the Wellcome Trust (grant number WT085949MA), the Spanish Research Council (CSIC) and the Spanish National Proteomics Institute (ProteoRed-ISC III) (grant number 2005X747_3), BMBF (SARA - FKZ 0315395F and BIOMARKERS - FKZ 01GI1104A).

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