title: MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.
abstract: MAGIC-web is the first web server, to the best of our knowledge, that performs both untargeted and targeted analyses of mass spectrometry-based glycoproteomics data for site-specific N-linked glycoprotein identification. The first two modules, MAGIC and MAGIC+, are designed for untargeted and targeted analysis, respectively. MAGIC is implemented with our previously proposed novel Y1-ion pattern matching method, which adequately detects Y1- and Y0-ion without prior information of proteins and glycans, and then generates in silico MS(2) spectra that serve as input to a database search engine (e.g. Mascot) to search against a large-scale protein sequence database. On top of that, the newly implemented MAGIC+ allows users to determine glycopeptide sequences using their own protein sequence file. The third module, Reports Integrator, provides the service of combining protein identification results from Mascot and glycan-related information from MAGIC-web to generate a complete site-specific protein-glycan summary report. The last module, Glycan Search, is designed for the users who are interested in finding possible glycan structures with specific numbers and types of monosaccharides. The results from MAGIC, MAGIC+ and Reports Integrator can be downloaded via provided links whereas the annotated spectra and glycan structures can be visualized in the browser. MAGIC-web is accessible from http://ms.iis.sinica.edu.tw/MAGIC-web/index.html.
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
authors.forename: T Mamie
authors.initials: TM
authors.lastname: Lih
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Wai-Kok
authors.initials: WK
authors.lastname: Choong
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.
authors.forename: Chen-Chun
authors.initials: CC
authors.lastname: Chen
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
authors.forename: Cheng-Wei
authors.initials: CW
authors.lastname: Cheng
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Hsin-Nan
authors.initials: HN
authors.lastname: Lin
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Ching-Tai
authors.initials: CT
authors.lastname: Chen
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
authors.forename: Hui-Yin
authors.initials: HY
authors.lastname: Chang
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Wen-Lian
authors.initials: WL
authors.lastname: Hsu
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan tsung@iis.sinica.edu.tw.
authors.forename: Ting-Yi
authors.initials: TY
authors.lastname: Sung
mesh_terms: D003198:Computer Simulation; D030562:Databases, Protein; D006020:Glycopeptides / Q000032:analysis / Q000737:chemistry; D006023:Glycoproteins / Q000032:analysis* / Q000737:chemistry*; D006801:Humans; D020407:Internet; D013058:Mass Spectrometry; D011134:Polysaccharides / Q000032:analysis* / Q000737:chemistry*; D040901:Proteomics; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D006020:Glycopeptides; D006023:Glycoproteins; D011134:Polysaccharides