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.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

“…MaXIC-Q provides quantitation analysis of large-scale datasets supporting SILAC, ICAT, and other labeling methods produced by users (Tsou et al, 2009). Implemented in Visual C + + , the latest release (0.9.2) can be run in two modes, via web or as a desktop application.…”

Existing bioinformatics tools for the quantitation of post-translational modifications

“…MaXIC-Q, a web application, uses extracted ion chromatograms (XIC) and projected ion mass spectra for generic SIL quantitation (Tsou et al 2009). In their study, the authors also confirmed interesting results using MS/MS measurements.…”