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ProteomicspLink 2: A high-speed search engine with systematic evaluation for proteome-scale identification of cross-linked peptides
Crosslinking mass spectrometry (CXMS) is a powerful technique to study protein structures and interactions. However, software tools for CXMS data analysis suffer from poor speed and credibility, especially at a proteome scale. Here, we introduce pLink 2, a search engine with higher speed and credibi...
ORGANISM(S): Escherichia coli 
2019-07-26 | PXD012109 | Pride
E.coli Qehf 
ProteomicsH3pT11 regulates histone homeostasis and replication-coupled nucleosome assembly
newly synthesized H3 is phosphorylated at T11 by the CPC complex, licensing Asf1 binding and nuclear import; upon nuclear entry, H3pT11 facilitates Rtt109-catalyzed H3K56 acetylation, which antagonizes Hat1 and promotes nucleosome assembly by CAF-1 and Rtt106 16; subsequently, Rtt101-mediated H3K122...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2026-08-05 | PXD077347 | Pride
H3k79me3 h3t11 phosphorylation histone homeostasis 
ProteomicsProteolytic Cleavage Activates the Mitochondrial Isoform of TOP3A
The TOP3A gene encodes two isoforms, one targeted to the nucleus and one to mitochondria. Nuclear TOP3A functions as part of the BTRR complex to resolve double Holliday junctions during homologous recombination, while the mitochondrial isoform separates hemicatenated daughter mitochondrial DNA molec...
ORGANISM(S): Homo sapiens (Human) 
2025-10-01 | PXD064926 | Pride
Top3a Mitochondria Mitochondrial processing peptidase (mmp) Proteolytic cleavage product 
ProteomicsIdentifying Cilary Proteins in Bovine Retinas using a Gentile Extraction Method
Mutations in retinal primary cilia are responsible for human blindness but the mechanisms are not fully understood. Characterizing the proteome of an organelle such as cilia, is a fruitful way to understand its function but methods often require considerable sample quantities. Here we develop a meth...
ORGANISM(S): Bos taurus (Bovine) 
2024-07-11 | PXD051952 | Pride
Bovine Rod outer segment Photoreceptor Retina Primary cilia 
ProteomicsImproving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data
Jurkat cell lysate was size-fractionated by gel-eluted fraction entrapment electrophoresis on a 12% gel (GELFrEE, Expedeon). Each fraction was analyzed by HPLC-ESI-MS/MS (nanoACQUITY, Waters and QE-HF, ThermoFisher Scientific).
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-05-15 | MSV000085414 | MassIVE
ProteomicsA Comprehensive Atlas of Protein Turnover Rates in Murine Tissues
Data for protein turnover rates in mammalian tissues
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2020-11-07 | MSV000086426 | MassIVE
ProteomicsInfluence of generational obesity on the visceral adipose proteome
Obesity is a global health concern affecting over 650 million adults with a major contributor being an increased consumption of a high-fat diet. Maternal obesity often results in an increased risk of offspring developing obesity. In this study, we examined the effect of diet on visceral adipose in ...
ORGANISM(S): Mus musculus (Mouse) 
2024-10-17 | PXD042092 | Pride
Proteomics Suspension trapping Generational obesity Omental tissue Adipose tissue Mouse Diet S-trap 
ProteomicsOpen-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics, part 2
Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry (MS/MS) data in shotgun proteomics are not successfully identified. We have developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-07-11 | PXD008783 | Pride
Open-pfind Yeast Q exactive hf Metabolically label 
ProteomicsSaccharomyces cerevisiae LC-MSMS
IP-MS detection of proteins pulled down by Glc7-FLAG by mass spectrometry
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-10-24 | PXD036005 | Pride
Lc-msms Saccharomyces cerevisiae 
ProteomicsSaccharomyces cerevisiae LC-MSMS
IP-MS detection of proteins pulled down by Ino80-FLAG by mass spectrometry
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-02-07 | PXD035908 | Pride
Lc-msms Saccharomyces cerevisiae 
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