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ProteomicsRe-analysis of glycoproteomics data with MSFragger-Glyco
Reanalysis of submissions PXD011533 and PXD009476 using MSFragger-Glyco mode. Processed MSFragger results files (pepXML) and PSM tables (psm.tsv) supporting MSFragger-Glyco manuscript (Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Recent advances in methods for enric...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2020-10-06 | PXD021196 | Pride
Glycosylation Glycoproteomics Msfragger Reanalysis O-glycosylation Glycan Glycopeptide N-glycosylation 
UnknownFast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco.
Not available
S-EPMC7606558 | biostudies-literature
ProteomicsAnalysis of O-glycoproteomics data with MS-Decipher, MetaMorpheus, MSFragger-Glyco and Mascot
We presented a user-friendly proteomic database search platform, MS-Decipher, for the identification of peptides from MS data. Two scoring schemes, rank score and hyperscore, could be used for peptide spectra matching. FDR controlling strategies could be used after searching, and it was found that M...
ORGANISM(S): Homo Sapiens (human) 
2022-01-13 | PXD027004 | JPOST Repository
UnknownGlyco-Decipher enables glycan database-independent peptide matching and in-depth characterization of site-specific N-glycosylation.
Not available
S-EPMC8990002 | biostudies-literature
ProteomicsQuantitative Mapping of the in vivo O-GalNAc Glycoproteome in Mouse Tissues
A large family of GalNAc transferases (GalNAc-Ts) catalyzes the covalent attachment of N-Acetylgalactosamine (GalNAc) to serine and threonine residues on proteins that pass through the secretory pathway in the first committed step of mucin-type O-glycosylation. Abnormalities in the activity of indi...
ORGANISM(S): Mus musculus (Mouse) 
2024-05-24 | PXD040196 | Pride
O-galnac Site-specific Glycoproteome Mouse tissues 
UnknownMultiattribute Glycan Identification and FDR Control for Glycoproteomics.
Not available
S-EPMC8933705 | biostudies-literature
ProteomicsRe-analysis of dataset PXD017646 by O-Search-Pattern and other tools
We adopted the method used in the O-Pair article to validate the FDR calculations of O-glycopeptide search in O-Search-Pattern, O-Pair Search, MSFragger-Glyco, and pGlyco. The detailed description of the method was provided in the ‘Methods’ and ‘Evaluating O-Pair Search performance’ parts of O-Pair ...
ORGANISM(S): Homo Sapiens (human) 
2023-05-31 | PXD039078 | JPOST Repository
UnknownLibrary-based virtual match-between-runs quantification in GlyPep-Quant improves site-specific glycan identification.
Not available
S-EPMC12259847 | biostudies-literature
ProteomicsExpanding glycopeptide identification with Match-Between-Glycans (MBG) in FragPipe
Glycosylation is one of the most important, but also most complex, post-translational modifications of proteins. Mass spectrometry-based glycoproteomics analysis offers a powerful approach to explore the fundamental roles of glycosylation, but achieving sufficient fragmentation for glycopeptide assi...
ORGANISM(S): Candida albicans (Yeast) Mus musculus (Mouse) Homo sapiens (Human) 
2026-09-01 | PXD074575 | Pride
Human plasma  glycoproteomics  n-glycopeptides  pasef  timstof  msfragger-glyco  fragpipe  ion mobility 
UnknownQuantitative proteome-wide O-glycoproteomics analysis with FragPipe.
Not available
S-EPMC11648966 | biostudies-literature
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