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The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.
Proteomics. 2015 Sep; 15(18):3152-62.P

Abstract

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/.

Authors+Show Affiliations

Institute of Integrative Biology, University of Liverpool, Liverpool, UK.The Faculty of Life Sciences, University of Manchester, Manchester, UK.The School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.Institute of Integrative Biology, University of Liverpool, Liverpool, UK.Institute of Integrative Biology, University of Liverpool, Liverpool, UK.Institute of Integrative Biology, University of Liverpool, Liverpool, UK.The School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.The Faculty of Life Sciences, University of Manchester, Manchester, UK.Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26037908

Citation

Qi, Da, et al. "The mzqLibrary--An Open Source Java Library Supporting the HUPO-PSI Quantitative Proteomics Standard." Proteomics, vol. 15, no. 18, 2015, pp. 3152-62.
Qi D, Zhang H, Fan J, et al. The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard. Proteomics. 2015;15(18):3152-62.
Qi, D., Zhang, H., Fan, J., Perkins, S., Pisconti, A., Simpson, D. M., Bessant, C., Hubbard, S., & Jones, A. R. (2015). The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard. Proteomics, 15(18), 3152-62. https://doi.org/10.1002/pmic.201400535
Qi D, et al. The mzqLibrary--An Open Source Java Library Supporting the HUPO-PSI Quantitative Proteomics Standard. Proteomics. 2015;15(18):3152-62. PubMed PMID: 26037908.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard. AU - Qi,Da, AU - Zhang,Huaizhong, AU - Fan,Jun, AU - Perkins,Simon, AU - Pisconti,Addolorata, AU - Simpson,Deborah M, AU - Bessant,Conrad, AU - Hubbard,Simon, AU - Jones,Andrew R, Y1 - 2015/07/14/ PY - 2014/11/14/received PY - 2015/05/02/revised PY - 2015/05/29/accepted PY - 2015/6/4/entrez PY - 2015/6/4/pubmed PY - 2016/6/22/medline KW - Bioinformatics KW - Data standard KW - MzQuantML KW - Proteomics standards initiative (PSI) KW - Software KW - XML SP - 3152 EP - 62 JF - Proteomics JO - Proteomics VL - 15 IS - 18 N2 - The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/. SN - 1615-9861 UR - https://www.unboundmedicine.com/medline/citation/26037908/The_mzqLibrary__An_open_source_Java_library_supporting_the_HUPO_PSI_quantitative_proteomics_standard_ L2 - https://doi.org/10.1002/pmic.201400535 DB - PRIME DP - Unbound Medicine ER -