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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




No version available


  • person_outline Andrew Jones

Publication for mzQuantML

mzQuantML citations


The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Genome Biol
PMCID: 5793360
PMID: 29386051
DOI: 10.1186/s13059-017-1377-x

[…] shed data standards are available, for instance, for representing raw MS data (the mzML data format []), peptide and protein identifications (mzIdentML [] and mzTab []), and quantitative information (mzQuantML [] and mzTab).The existence of compatible and interoperable data formats is a way to facilitate and advance “multi-omics” studies [], and a clear need in proteogenomics, due to the growing i […]


Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

J Proteome Res
PMCID: 5715286
PMID: 28849660
DOI: 10.1021/acs.jproteome.7b00370

[…] ned a new CV called XLMOD.In many proteomics pipelines, different workflows and software are used for quantification, and the needs for data storage are rather different from identification data. The mzQuantML format (stable version 1.0) was designed to store the outputs of quantification software from a variety of popular discovery-based workflows including MS1- and MS2-based label-free, MS1 labe […]


Exploring the potential of public proteomics data

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

[…] as 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 […]


The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

PMCID: 4973685
PMID: 26037908
DOI: 10.1002/pmic.201400535

[…] es in a sub‐set group. Protein abundance data is then calculated according to the user selected method (sum, mean, median of peptide abundance values) and output as a protein group list in the output mzQuantML file, which includes the protein group information and the AssayQuantLayers (e.g. protein group raw abundance and protein group normalised abundance). More advanced protocols for protein qua […]


Representation of selected reaction monitoring data in the mzQuantML data standard

PMCID: 4692094
PMID: 25884107
DOI: 10.1002/pmic.201400281

[…] e ProteomeXchange consortium [], under which umbrella the PRIDE [] database accepts submissions for “discovery” or global analyses, and the PASSEL repository accepts quantitative SRM datasets [].When mzQuantML was initially released [], the specifications contained four sets of “semantic rules” checked by the validation software [] to support (i) intensity-based (MS1) label free, (ii) MS1 label-ba […]


COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

PMCID: 4605977
PMID: 26491418
DOI: 10.1007/s11306-015-0810-y

[…] n and metabolite identification, to the experimental metadata. We aim to extend the open standards for MS data exchange initiated by PSI, such as mzML (Martens et al. ), mzIdentML (Jones et al. ) and mzQuantML (Walzer et al. ) to meet the requirement of metabolomics experiments for reporting MS experiments. One example are GC–MS based metabolomics experiments, where data are often available in eit […]


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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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