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ProteomicsDeciphering O-glycoprotease substrate preferences with O-Pair Search
O-glycoproteases are an emerging class of enzymes that selectively digest glycoproteins at positions decorated with specific O-linked glycans. O-glycoprotease substrates range from any O-glycoprotein (albeit with specific O-glycan modifications) to only glycoproteins harboring specific O-glycosylate...
ORGANISM(S): Homo sapiens (Human) 
2023-02-15 | PXD035775 | Pride
O-glycoproteomics Glycoproteins Cleavage Glycoproteomics Informatics O-pair search O-glycoprotease 
UnknownDeciphering <i>O</i>-glycoprotease substrate preferences with O-Pair Search.
Not available
S-EPMC10010678 | 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
TranscriptomicsA search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.
Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumu...
ORGANISM(S): Staphylococcus aureus 
2010-05-18 | E-GEOD-17135 | biostudies-arrayexpress
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 
ProteomicsRe-analysis of dataset PXD017646
We adopted the method used in the O-Pair article to validate the FDR calculations of O-glycopeptide search in MS-Decipher. The detailed description of the method was provided in the ‘Methods’ and ‘Evaluating O-Pair Search performance’ parts of O-Pair article (Lu et al., 2020). The results were firs...
ORGANISM(S): Homo Sapiens (human) 
2022-01-13 | PXD029863 | JPOST Repository
ProteomicsAutonomous Dissociation-type Selection for Glycoproteomics using a Real-Time Library Search
Tandem mass spectrometry (MS/MS) is the gold standard for intact glycopeptide identification, enabling peptide sequence elucidation and site-specific localization of glycan compositions. Beam-type collisional activation is generally sufficient for N-glycopeptides, while electron-driven dissociation ...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2024-11-15 | PXD055054 | Pride
N-glycopeptides Glycoproteomics Intelligent data acquisition Tandem mass spectrometry Beam-type collisional dissociation O-glycopeptides Product-dependent triggering Real-time library search Electron transfer dissociation 
ProteomicsMS1Connect: a mass spectrometry run similarity measure
Researchers may be interested in finding proteomics runs, which have been deposited into online repositories, that are similar to their own data. However, it is difficult to measure the similarity of a pair of proteomics runs. Here, we present a new method, MS1Connect, that only uses intact peptide ...
ORGANISM(S): Porphyrobacter sp. WLSH-3 Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 Nicotiana benthamiana Bacillus thuringiensis Escherichia coli Bacillus cereus Bacillus thuringiensis str. Al Hakam 
2023-01-05 | PXD027791 | Pride
Bacteria Similarity 
UnknownQuantitative proteome-wide O-glycoproteomics analysis with FragPipe.
Not available
S-EPMC11648966 | biostudies-literature
ProteomicsCell-type-specific labeling and profiling of glycans in living mice
Metabolic labeling of glycans with clickable unnatural sugars has enabled glycan imaging and glycoproteomics in mixed cell populations. However, in vivo labeling and profiling of cell-type-specific glycans remains challenging. Here, we develop genetically encoded metabolic glycan labeling (GeMGL),...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2022-02-28 | PXD030663 | Pride
Metabolic glycan labeling Cell-type-specific Glycan 
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