Format

Send to

Choose Destination
Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):88-97. doi: 10.1016/j.bbapap.2013.04.004. Epub 2013 Apr 12.

A tutorial for software development in quantitative proteomics using PSI standard formats.

Author information

1
Institute of Integrative Biology, University of Liverpool, Liverpool, UK. Electronic address: F.Galarza@liv.ac.uk.

Abstract

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.

KEYWORDS:

APIs; Quantitative proteomics; Software; Standard formats

PMID:
23584085
PMCID:
PMC4008935
DOI:
10.1016/j.bbapap.2013.04.004
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center