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 MS2 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.
Highlights
Protein glycosylation involves numerous biological relevant events, such as cell adhesion [1,2], protein folding [3] and immune responses [4]
Given an intact glycopeptide MS2 spectrum, our previously proposed method using two novel triplet peak patterns for Y1-ion detection, called Trident, is applied to detect two sets of triplet peaks that are matched to consecutive mass losses of either two GlcNAc’s or the dissociation of an NH3 followed by a GlcNAc and to determine the Y0-ion [17]
Reports Integrator combines the results from MAGIC/MAGIC+ and Mascot for more detailed information of identified glycoproteins/glycopeptides
Summary
Protein glycosylation involves numerous biological relevant events, such as cell adhesion [1,2], protein folding [3] and immune responses [4]. It is a commonest and highly complex post-translation modification that alterations in glycosylation are observed in association with cancers [5,6], inherited disorders [7,8] and other diseases [9]. Applying tandem MS to analyse intact glycopeptides retaining site-specific glycans has the advantage of possible inference of glycosylation sites and glycan compositions. We have developed MAGIC-web to provide automated site-specific N-linked glycosylation analysis from acquired beam-type CID MS2 data for both untargeted and targeted glycoprotein identification. MAGIC (Mass spectrometry-based Automated Glycopeptide IdentifiCation platform) is previously published as a stand-alone program executable on the Windows
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