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MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS.

ABSTRACT: 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.

SUBMITTER: Tsou CC

PROVIDER: S-EPMC2703943 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS.

Tsou Chih-Chiang CC Tsui Yin-Hao YH Yian Yi-Hwa YH Chen Yi-Ju YJ Yang Han-Yin HY Yu Chuan-Yih CY Lynn Ke-Shiuan KS Chen Yu-Ju YJ Sung Ting-Yi TY Hsu Wen-Lian WL

Nucleic acids research 20090615 Web Server issue

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 m ...[more]

PMID: 19528069

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Dataset Information

MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS.

Publications

MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS.

Similar Datasets

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