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 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.

Large-scale intact glycopeptide identification by Mascot database search

“…The FDR estimation for intact glycopeptide identifications is debatable and especially in case of glycopeptide identifications in relatively small numbers, the accurate estimation of FDR values is not possible. Moreover, FDR control of both glycan and peptide identifications is challenging and based on the analytical workflow used, some customized strategies have been proposed 35 , 36 . Provided fragmentation information of both peptide and glycans of all the glycopeptides, FDR tools provided in Mascot can be confidently used.…”

Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis

“…Some subsequently developed software tools, such as pGlyco ( 61 ), glyXtoolMS ( 67 ), and GPSeeker ( 68 ), conduct simple mass spectrum annotation steps. A web server, MAGIC-web ( 69 ), which was established by the MAGIC ( 44 ) software development team, enables mass spectrum annotation and glycan structure visualization. This function was designed as one of the functional modules on the web server and not integrated into the search engine of MAGIC and MAGIC+, requiring users have to complete additional operation themselves.…”

Glycoprotein Enrichment Analytical Techniques

“…Park et al developed a robust software package, Integrated GlycoProteome Analyzer (I-GPA), to analyze and map N-glycoproteomes; their method identified 600+ N-glycopeptides and quantified ~600 N-glycopeptides from human plasma with an astonishing 0% false positive discovery rate manually verified (Park, Kim, Hwang, Lee, Ahn, Lee, et al, 2016). Lih et al developed MAGIC-web, a web server dedicated to targeted and untargeted N-linked glycan analysis (Lih, Choong, Chen, Cheng, Lin, Chen, et al, 2016). Zeng et al developed pGlyco to identify N-glycans from HCD-MS/MS and CID-MS/MS data sets; a novel target decoy method was implemented to estimate FDR of glycan identification (W.…”