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dc.contributor.authorDomagalski, Marcin Jakub
dc.contributor.authorAlocci, Davide
dc.contributor.authorAlmeida, Andreia
dc.contributor.authorKolarich, Daniel
dc.contributor.authorLisacek, Frederique
dc.date.accessioned2018-07-30T01:30:25Z
dc.date.available2018-07-30T01:30:25Z
dc.date.issued2018
dc.identifier.issn1862-8346
dc.identifier.doi10.1002/prca.201700069
dc.identifier.urihttp://hdl.handle.net/10072/376733
dc.description.abstract1 Purpose: PepSweetener is a web‐based visualization tool designed to facilitate the manual annotation of intact glycopeptides from MS data regardless of the instrument that produced these data. 2 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. 3 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. 4 Conclusions and clinical relevance: PepSweetener efficiently allows the selection of the most probable intact glycopeptide mass matches and speeds up the verification process. It is 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/).
dc.description.peerreviewedYes
dc.languageEnglish
dc.language.isoeng
dc.publisherWiley-VCH Verlag
dc.relation.ispartofpagefrom1700069-1
dc.relation.ispartofpageto1700069-10
dc.relation.ispartofjournalProteomics - Clinical Applications
dc.subject.fieldofresearchBiochemistry and cell biology not elsewhere classified
dc.subject.fieldofresearchMedical biochemistry and metabolomics
dc.subject.fieldofresearchGlycobiology
dc.subject.fieldofresearchGlycoconjugates
dc.subject.fieldofresearchProteomics and intermolecular interactions (excl. medical proteomics)
dc.subject.fieldofresearchBioinformatics and computational biology
dc.subject.fieldofresearchcode310199
dc.subject.fieldofresearchcode3205
dc.subject.fieldofresearchcode310107
dc.subject.fieldofresearchcode340405
dc.subject.fieldofresearchcode310109
dc.subject.fieldofresearchcode3102
dc.titlePepSweetener: A Web-Based Tool to Support Manual Annotation of Intact Glycopeptide MS Spectra
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.description.notepublicThis publication has been entered into Griffith Research Online as an Advanced Online Version.
gro.hasfulltextNo Full Text
gro.griffith.authorKolarich, Daniel
gro.griffith.authorFerreira de Almeida, Andreia F.


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