Nucleic Acids Research Advance Access originally published online on June 15, 2009
Nucleic Acids Research 2009 37(Web Server issue):W661-W669; doi:10.1093/nar/gkp476
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W661-W669
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC–MS
1Institute of Information Science and 2Institute of Chemistry, Academia Sinica, Nankang, Taipei, Taiwan 115
*To whom correspondence should be addressed. Tel: +886 2 27883799, Ext: 1711; Fax: +886 2 27824814; Email: tsung{at}iis.sinica.edu.tw
Correspondence may also be addressed to Wen-Lian Hsu. Email: hsu{at}iis.sinica.edu.tw
Received February 17, 2009. Revised April 28, 2009. Accepted May 17, 2009.
Isotope labeling combined with liquid chromatography–mass spectrometry (LC–MS) provides a robust platform for analyzing differential protein expression in proteomics research. We present a web service, called MaXIC-Q Web (http://ms.iis.sinica.edu.tw/MaXIC-Q_Web/), for quantitation analysis of large-scale datasets generated from proteomics experiments using various stable isotope-labeling techniques, e.g. SILAC, ICAT and user-developed labeling methods. It accepts spectral files in the standard mzXML format and search results from SEQUEST, Mascot and ProteinProphet as input. Furthermore, MaXIC-Q Web uses statistical and computational methods to construct two kinds of elution profiles for each ion, namely, PIMS (projected ion mass spectrum) and XIC (extracted ion chromatogram) from MS data. Toward accurate quantitation, a stringent validation procedure is performed on PIMSs to filter out peptide ions interfered with co-eluting peptides or noise. The areas of XICs determine ion abundances, which are used to calculate peptide and protein ratios. Since MaXIC-Q Web adopts stringent validation on spectral data, it achieves high accuracy so that manual validation effort can be substantially reduced. Furthermore, it provides various visualization diagrams and comprehensive quantitation reports so that users can conveniently inspect quantitation results. In summary, MaXIC-Q Web is a user-friendly, interactive, robust, generic web service for quantitation based on ICAT and SILAC labeling techniques.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.