title: 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.
authors.affiliation: Institute of Information Science and Institute of Chemistry, Academia Sinica, Nankang, Taipei, Taiwan 115.
authors.forename: Chih-Chiang
authors.initials: CC
authors.lastname: Tsou
authors.forename: Yin-Hao
authors.initials: YH
authors.lastname: Tsui
authors.forename: Yi-Hwa
authors.initials: YH
authors.lastname: Yian
authors.forename: Yi-Ju
authors.initials: YJ
authors.lastname: Chen
authors.forename: Han-Yin
authors.initials: HY
authors.lastname: Yang
authors.forename: Chuan-Yih
authors.initials: CY
authors.lastname: Yu
authors.forename: Ke-Shiuan
authors.initials: KS
authors.lastname: Lynn
authors.forename: Yu-Ju
authors.initials: YJ
authors.lastname: Chen
authors.forename: Ting-Yi
authors.initials: TY
authors.lastname: Sung
authors.forename: Wen-Lian
authors.initials: WL
authors.lastname: Hsu
mesh_terms: D002853:Chromatography, Liquid; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D042783:Endothelial Cells / Q000378:metabolism; D020407:Internet; D007553:Isotope Labeling; D013058:Mass Spectrometry; D017942:Nitric Acid / Q000378:metabolism; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000032:analysis*; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D011506:Proteins; D017942:Nitric Acid