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ProteomicsProteome-wide identifying site non-specific cross-linking peptides with SpotLink
We developed SpotLink to identify site non-specific cross-links from the proteome scale. Here described the Abeta dataset and the HeLa dataset to evaluate SpotLink.
ORGANISM(S): Homo sapiens (Human) 
2022-08-25 | PXD030274 | Pride
Spotlink Cross-linking Cx-ms Site non-specific Cl-ms Proteome 
ProteomicsAn automated intact glycopeptide enrichment method for serum site-specific N-glycoproteomic analysis
We developed an automated glycopeptide enrichment method for the analysis of serum site-specific N-glycoproteome. This automated method allowed for processing one sample within 20 min. It showed higher enrichment specificity, more intact glycopeptide identifications, and better quantitative reproduc...
ORGANISM(S): Homo Sapiens (human) 
2021-04-06 | PXD025151 | JPOST Repository
TranscriptomicsSaccharomyces cerevisiae 3' poly(A) site mapping
The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented ef...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-10 | E-GEOD-40110 | biostudies-arrayexpress
TranscriptomicsU2AF1 mutations alter splice site recognition in hematological malignancies
Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 altered its normal role in RNA splicing. W...
ORGANISM(S): Homo sapiens 
2014-09-23 | E-GEOD-58871 | biostudies-arrayexpress
ProteomicsSite-selective photo crosslink to methyllysine readers via single electron transfer between sulfonium and tryptophan
Reader proteins play significant roles in cell signaling from site-specific lysine methylation, but the progress of new reader investigations is rather slow. Photoreactive crosslinkers enable reader identifications, but it requires laborious chemical synthesis for optimization of the photoreactive g...
ORGANISM(S): Homo Sapiens 
2024-02-04 | PXD049149 |
ProteomicsSite-Specific Competitive Kinase Inhibitor Target Profiling Using Phosphonate Affinity Tags
Protein kinases are prime targets for drug development due to their involvement in various cancers. However, selective inhibition of kinases, while avoiding off-target effects remains a significant challenge for the development of protein kinase inhibitors. Activity-based protein profiling (ABPP), i...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD058749 | Pride
Chemical proteomics  activity-based protein profiling  site-specific  protein kinase inhibitor profiling  ephrin receptor inhibitor  nvp-bhg712 
ProteomicsSite-specific Extraction of O-linked glycopeptides (EXoO) Maps Landscape of In Vivo O-linked Glycoproteome
Protein glycosylation is one of the most common protein modifications and plays essential roles in biology and therapeutics. However, the analysis of in vivo O-linked glycosylation, a major type of protein glycosylation, has been severely impeded by the scarcity of technology. Here, a chemoenzymatic...
ORGANISM(S): Homo sapiens (Human) 
2018-12-05 | PXD009476 | Pride
Site-specific Glycosylation Exoo In vivo O-linked 
TranscriptomicsMolecular characterization of the chromosome 7 in SMZL
Splenic marginal zone lymphomas (SMZL) are an uncommon type of B-cell non-Hodgkin’s lymphoma (NHL-B) in which no specific chromosomal translocations have been described. In contrast, the most frequent cytogenetic abnormality is the loss of the long arm of chromosome 7 (7q). Previous reports have loc...
ORGANISM(S): Homo sapiens 
2011-10-10 | E-GEOD-31203 | biostudies-arrayexpress
GenomicsMechanisms of PU.1 binding site selection in-vivo
The majority of sequence-specific transcription factors bind genomic DNA only at a fraction of their potential binding sites and the ‘rules’ for binding or not-binding are only partially understood. Here, we studied the binding properties of the myeloid and B-cell specific transcription factor PU.1 ...
ORGANISM(S): Homo sapiens 
2013-05-15 | E-GEOD-43098 | biostudies-arrayexpress
ProteomicsIdentification of conjugation site of T-DM1
Ado-trastuzumab emtansine(T-DM1) is manufactured by conjugating DM1 to lysine of Trastuzumab via a non-cleavable linker in a non-specific mode.conjugated site of T-DM1 were identified using a bottom-up strategy through LC-HR-MS/MS.
ORGANISM(S): Homo sapiens environmental sample 
2025-03-05 | PXD054136 | Pride
Conjugation site Lc-ms/ms 
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