biostudies-literatureUnknown44(W1)Lih TMMAGIC-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 filNucleic acids researchW575-80https://www.ebi.ac.uk/biostudies/studies/S-EPMC4987873biostudies-literatureMAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.PMC4987873Sung TYCheng CWChang HYChoong WKChen CTLih TMChen CCHsu WLLin HNfalseMAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.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 fil2016-01-01T00:00:00Z2016 Jul2025-04-04T10:35:22.976Z2019-03-27T02:20:51ZS-EPMC49878732708494310.1093/nar/gkw254