Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
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- 作者：Yasset Perez-Riverol ; Rui Wang ; Henning Hermjakob ; Markus M眉ller ; Vladimir Vesada ; Juan Antonio Vizca铆no
- 关键词：AMT ; Accurate Mass Tag ; ATAQS ; Automated and Targeted Analysis with Quantitative SRM ; CV ; Controlled Vocabulary ; DAO ; Data Access Object ; EBI ; European Bioinformatics Institute ; emPAI ; exponentially modified Protein Abundance Index ; FDR ; False Discovery Rate ; (HUPO)-PSI ; (Human Proteome Organization) &mdash ; Proteomics Standards Initiative ; GUI ; Graphical User Interface ; ICAT ; Isotope-Coded Affinity Tags ; ICPL ; Isotope-Coded Protein Label ; IPTL ; Isobaric Peptide Termini Labeling ; ISB ; Institute
- 刊名：Biochimica et Biophysica Acta - Proteins and Proteomics
- 出版年：January, 2014
- 年：2014
- 卷：1844
- 期：1_part_PA
- 页码：63-76
- 全文大小：835 K
文摘
Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.