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ProteomicsiBench Ground Truth Validation Tool 2.0
iBench is an open-source tool that provides enhanced validation of Mass Spectrometry identification methods. In this updated version, iBench 2.0 takes high confidence peptide identifications from previously measured MS data and embeds the sequences in an in silico-only proteome as spliced or non-spl...
ORGANISM(S): Homo sapiens (Human) 
2023-12-21 | PXD044451 | Pride
Mass spectrometry 20s proteasomes Benchmarking Mhc-i presentation Pcps 
ProteomicsDNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)
MutLα, a heterodimer consisting of MLH1 and PMS2, is a key player of DNA mismatch repair (MMR), yet little is known about its regulation. In this study, we used mass spectrometry to identify phosphorylated residues within MLH1 and PMS2. The most frequently detected phosphorylated amino acid was seri...
ORGANISM(S): Homo sapiens (Human) 
2018-08-28 | PXD009524 | Pride
Ck2 Phosphorylation Lynch syndrome Dna mismatch repair Mutlα Mlh1 
ProteomicsQuantitative (Glyco-)Proteomics of Haloferax volcanii Biofilm Formation
A quantitative proteomics analysis comparing planktonic and sessile cells at different stages of biofilm development, using iTRAQ labeling, has been performed for Haloferax volcanii. Samples were taken from liquid, shaking cultures were compared to samples from static cultures, separated into sessil...
ORGANISM(S): Haloferax volcanii (Halobacterium volcanii) 
2020-05-11 | PXD011012 | Pride
Glycosylation Haloferax volcanii Biofilm Itraq 
ProteomicsHypoxia-induced changes in SUMO conjugation affect transcriptional regulation under low oxygen
Recent data support that sumoylation, the covalent attachment of the Small Ubiquitin-related MOdifier (SUMO) to proteins, is involved in the activation of the hypoxic response and the ensuing signalling cascade. To gain insights into differences of the SUMO1 and SUMO2/3 proteome of HeLa cells under ...
ORGANISM(S): Homo sapiens (Human) 
2019-04-03 | PXD010946 | Pride
Mass spectrometry Silac Hypoxia Sumo 
ProteomicsConformational rearrangements upon start codon recognition in human 48S translation initiation complex
Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct...
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD031985 | Pride
Ribosome 48s initiation comples Eif1 
ProteomicsA small RNA and its involvement in zinc transport
The function and mode of action of small regulatory RNAs is currently still understudied in archaea. In the halophilic archaeon H. volcanii a plethora of sRNAs have been identified, however, in-depth functional analysis is missing for most of them. We selected a small RNA (s479) from H. volcanii for...
ORGANISM(S): Haloferax volcanii (Halobacterium volcanii) 
2021-08-10 | PXD022750 | Pride
Proteomics Abc transporter Archaea Metallostasis Transcriptomics Small rnas 
ProteomicsDithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions
In the present paper, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. To prove this three model systems, a) a small synthetic peptide from smB'/B protein incubated with U1snRNA oligonucleotide, b) in vitro reconstituted 15.5K protein with U4 snRNA oligonucleotide and c) nativ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2015-10-13 | PXD002656 | Pride
Dtt 
ProteomicsHaloferax volcanii Proteome Response to Deletion of a Rhomboid Protease Gene
Rhomboids are conserved intramembrane serine proteases involved in cell signaling processes. Their role in prokaryotes is scarcely known and remains to be investigated in Archaea. We previously constructed a rhomboid homologue deletion mutant (ΔrhoII) in Haloferax volcanii, which showed reduced moti...
ORGANISM(S): Haloferax volcanii DS2 
2020-05-14 | PXD011218 | Pride
Shotgun proteomics Archaea Haloferax volcanii Rhomboid protease Protease substrate 
ProteomicsThe response of Haloferax volcanii to salt and temperature stress: a proteome study by label-free mass spectrometry
We performed an in-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii under standard, low and high salt and low and high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high pH/reversed phase fractionated ...
ORGANISM(S): Haloferax volcanii DS2 
2019-09-04 | PXD011056 | Pride
Swath Haloferax volcanii Mass spectrometry Stress response Archaea Proteome 
ProteomicsNpl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA
RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate several functions at once and likely impact the structural integrity of the large mRNP assemblies, these...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-03-11 | PXD035153 | Pride
Rna-binding sites Npl3 Sr-like protein Mrnp assembly Structure Xl-ms Rna-binding proteins Nmr Mrna Gene expression 
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