Gonzalez-Galarza Faviel F, Qi Da, Fan Jun, Bessant Conrad, Jones Andrew R
Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):88-97. doi: 10.1016/j.bbapap.2013.04.004. Epub 2013 Apr 12.
The Human Proteome Organisation - Proteomics Standards Initiative (HUPO-PSI) has been working for ten years on the development of standardised formats that facilitate data sharing and public database deposition. In this article, we review three HUPO-PSI data standards - mzML, mzIdentML and mzQuantML, which can be used to design a complete quantitative analysis pipeline in mass spectrometry (MS)-based proteomics. In this tutorial, we briefly describe the content of each data model, sufficient for bioinformaticians to devise proteomics software. We also provide guidance on the use of recently released application programming interfaces (APIs) developed in Java for each of these standards, which makes it straightforward to read and write files of any size. We have produced a set of example Java classes and a basic graphical user interface to demonstrate how to use the most important parts of the PSI standards, available from http://code.google.com/p/psi-standard-formats-tutorial. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
人类蛋白质组组织-蛋白质组学标准倡议（HUPO-PSI）十年来一直致力于开发标准化格式，以促进数据共享和存入公共数据库。在本文中，我们回顾了三种HUPO-PSI数据标准——mzML、mzIdentML和mzQuantML，它们可用于设计基于质谱（MS）的蛋白质组学中的完整定量分析流程。在本教程中，我们简要描述了每个数据模型的内容，足以让生物信息学家设计蛋白质组学软件。我们还为最近用Java开发的针对这些标准的每个应用程序编程接口（API）的使用提供指导，这使得读取和写入任何大小的文件都很简单。我们编写了一组示例Java类和一个基本图形用户界面，以演示如何使用PSI标准的最重要部分，可从http://code.google.com/p/psi-standard-formats-tutorial获取。本文是名为：鉴定后时代的计算蛋白质组学的特刊的一部分。客座编辑：Martin Eisenacher和Christian Stephan。
