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.

Figure 1.

Pipeline of quantitation analysis using MaXIC-Q Web.

Figure 2.

Construction of the PIMS and XIC: (A) PIMS and (B) XIC.

Figure 3.

An example of peptide co-elution from the dataset of NO-treated endothelial cells: (A) Elution3D diagram, PIMS and XIC; (B) heavy-labeled peptide ion; and (C) light-labeled peptide ion of the peptide VTCPNHPDAILVEDYR.

Figure 4.

Cumulative distribution of proteins versus the standard error of ion ratios in the comparative study of NO-treated endothelial cells.

Figure 5.

Interface for file assignment.

Figure 6.

Interface for light- and heavy-label configuration.

Figure 7.

Quantitation result page.

Figure 8.

Example of (A) Elution3D, (B) XIC and (C) PIMS diagrams.