Proteomics - Clinical Applications
Proteomics - Clinical Applications
5 years ago

PepSweetener: A Web-Based Tool to Support Manual Annotation of Intact Glycopeptide MS Spectra

Davide Alocci, Marcin Jakub Domagalski, Frédérique Lisacek, Daniel Kolarich, Andreia Almeida
Purpose : PepSweetener is a web-based visualization tool designed to facilitate the manual annotation of intact glycopeptides from mass spectrometry (MS) data regardless of the instrument that produced this data. Experimental design : This exploratory tool uses a theoretical glycopeptide dataset to visualize all peptide-glycan combinations that fall within the error range of the query precursor ion. PepSweetener simplifies the determination of the correct peptide and glycan composition of a glycopeptide based on its precursor mass. The theoretical glycopeptide search space can be customized in an advanced query mode that specifies potential proteins/peptides, glycan compositions and several experimental parameters. Results : PepSweetener displays the results on an interactive heat-map chart where theoretical glycopeptide tile colors correspond to ppm deviations from the query precursor mass. Additionally, a visualization chart incorporates glycan composition filtering, sorting by mass and tolerance, and an in silico peptide fragmentation diagram is provided to further support the correct glycopeptide identification. Conclusions and clinical relevance : PepSweetener efficiently allows the selection of the most probable intact glycopeptide mass matches and speeds up the verification process. It was validated on serum protein samples and immunoglobulins. The tool is publicly hosted on ExPASy, the SIB Swiss Institute of Bioinformatics resource portal (http://glycoproteome.expasy.org/pepsweetener/app/). This article is protected by copyright. All rights reserved

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/prca.201700069

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