ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

被引：27

作者：

Perez-Riverol, Yasset ^{[1
]}

Uszkoreit, Julian ^{[2
]}

Sanchez, Aniel ^{[3
]}

Ternent, Tobias ^{[1
]}

del Toro, Noemi ^{[1
]}

Hermjakob, Henning ^{[1
]}

Vizcaino, Juan Antonio ^{[1
]}

Wang, Rui ^{[1
]}

机构：

[1] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England

[2] Ruhr Univ Bochum, Med Proteom Zenter, Med Bioinformat, ZKF, D-44801 Bochum, Germany

[3] Ctr Genet Engn & Biotechnol, Dept Prote, Havana, Cuba

来源：

BIOINFORMATICS | 2015年 / 31卷 / 17期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

SPECTROMETRY-BASED PROTEOMICS; MASS;

D O I：

10.1093/bioinformatics/btv250

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources. Finally, we present a set of algorithms and tools whose implementation illustrates the simplicity of developing applications using the library.

引用

页码：2903 / 2905

页数：3

共 10 条

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