title: SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis.
abstract: Glycoproteomics has rapidly become an independent analytical platform bridging the fields of glycomics and proteomics to address site-specific protein glycosylation and its impact in biology. Current glycopeptide characterization relies on time-consuming manual interpretations and demands high levels of personal expertise. Efficient data interpretation constitutes one of the major challenges to be overcome before true high-throughput glycopeptide analysis can be achieved. The development of new glyco-related bioinformatics tools is thus of crucial importance to fulfill this goal. Here we present SweetNET: a data-oriented bioinformatics workflow for efficient analysis of hundreds of thousands of glycopeptide MS/MS-spectra. We have analyzed MS data sets from two separate glycopeptide enrichment protocols targeting sialylated glycopeptides and chondroitin sulfate linkage region glycopeptides, respectively. Molecular networking was performed to organize the glycopeptide MS/MS data based on spectral similarities. The combination of spectral clustering, oxonium ion intensity profiles, and precursor ion m/z shift distributions provided typical signatures for the initial assignment of different N-, O- and CS-glycopeptide classes and their respective glycoforms. These signatures were further used to guide database searches leading to the identification and validation of a large number of glycopeptide variants including novel deoxyhexose (fucose) modifications in the linkage region of chondroitin sulfate proteoglycans.
authors.affiliation: Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden.
authors.forename: Waqas
authors.initials: W
authors.lastname: Nasir
authors.affiliation: Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden.
authors.forename: Alejandro Gomez
authors.initials: AG
authors.lastname: Toledo
authors.affiliation: Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Noborn
authors.affiliation: Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden.
authors.forename: Jonas
authors.initials: J
authors.lastname: Nilsson
authors.affiliation: Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States.
authors.forename: Mingxun
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States.
authors.forename: Nuno
authors.initials: N
authors.lastname: Bandeira
authors.affiliation: Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden.
authors.forename: Göran
authors.initials: G
authors.lastname: Larson
mesh_terms: D002809:Chondroitin Sulfates / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D006020:Glycopeptides / Q000032:analysis*; D006031:Glycosylation; D019158:N-Acetylneuraminic Acid / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D053719:Tandem Mass Spectrometry; D057188:Workflow
chemical_list: D006020:Glycopeptides; D002809:Chondroitin Sulfates; D019158:N-Acetylneuraminic Acid
keywords: MS/MS molecular networking; bioinformatics; chondroitin sulfate proteoglycans; fucose; glycopeptides; glycosylation; mass spectrometry; oxonium ion