Result: The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

Title:
The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.
Authors:
Qi D; Institute of Integrative Biology, University of Liverpool, Liverpool, UK., Zhang H; The Faculty of Life Sciences, University of Manchester, Manchester, UK., Fan J; The School of Biological and Chemical Sciences, Queen Mary University of London, London, UK., Perkins S; Institute of Integrative Biology, University of Liverpool, Liverpool, UK., Pisconti A; Institute of Integrative Biology, University of Liverpool, Liverpool, UK., Simpson DM; Institute of Integrative Biology, University of Liverpool, Liverpool, UK., Bessant C; The School of Biological and Chemical Sciences, Queen Mary University of London, London, UK., Hubbard S; The Faculty of Life Sciences, University of Manchester, Manchester, UK., Jones AR; Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
Source:
Proteomics [Proteomics] 2015 Sep; Vol. 15 (18), pp. 3152-62. Date of Electronic Publication: 2015 Jul 14.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 101092707 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1615-9861 (Electronic) Linking ISSN: 16159853 NLM ISO Abbreviation: Proteomics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Weinheim, Germany : Wiley-VCH,
MeSH Terms:
Database Management Systems* , Software*, Databases, Protein/*standards , Proteomics/*methods , Proteomics/*standards
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Grant Information:
BB/I000631/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/I00095X/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; B/I000631/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/K01997X/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council
Contributed Indexing:
Keywords: Bioinformatics; Data standard; MzQuantML; Proteomics standards initiative (PSI); Software; XML
Entry Date(s):
Date Created: 20150604 Date Completed: 20160621 Latest Revision: 20250529
Update Code:
20250530
PubMed Central ID:
PMC4973685
DOI:
10.1002/pmic.201400535
PMID:
26037908
Database:
MEDLINE

Further Information

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/.
(© 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)