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UnknownEnhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal.
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S-EPMC8259620 | biostudies-literature
ProteomicsAltered N-glycan composition impacts flagella mediated adhesion in Chlamydomonas reinhardtii
For the unicellular alga Chlamydomonas reinhardtii, the presence of N-glycosylated proteins on the surface of two flagella is crucial for both cell-cell interaction during mating and flagellar surface adhesion. However, it is not known whether only the presence or also the composition of N-glycans a...
ORGANISM(S): Chlamydomonas reinhardtii 
2020-12-22 | PXD018353 | Pride
Adhesion Sugarpy Prm Chlamydomonas reinhardtii N-glycosylation Flagella Lc-ms/ms 
ProteomicsPeptideForest: Semi-supervised machine learning integrating multiple search engines for peptide identification
We introduce PeptideForest, a semi-supervised machine learning approach that integrates the assignment of peptides to mass spectra from multiple algorithms to train a random forest classifier, thereby combining the results from different search engines. PeptideForest increases the number of peptide-...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2025-06-02 | PXD056915 | Pride
Human Machine learning E. coli Statistical post-processing Peptide identification 
ProteomicsComparative, quantitative proteomic analysis of cell shape transitions in Haloferax volcanii
Cell shape plays a crucial role in microbial survival. While Haloferax volcanii, a model haloarchaeon, forms rods and disks, depending on environmental conditions, little is known about mechanisms underpinning archaeal cell-shape determination. We identified mutants that exclusively form rods and ca...
ORGANISM(S): Haloferax volcanii (Halobacterium volcanii) Archaea 
2024-02-17 | PXD040781 | Pride
Archaeal proteome project Ursgal Archaea Haloferax volcanii Label-free quantification Cell shape 
ProteomicsCerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis
Meningitis is a life-threatening condition characterized by the inflammation of the leptomeningeal membranes surrounding the brain and spinal cord. The term meningitis is an umbrella term and includes several different etiologies. Acute bacterial meningitis (ABM) is one of the leading causes of deat...
ORGANISM(S): Streptococcus pyogenes M1 GAS Streptococcus agalactiae serogroup V Pseudomonas aeruginosa PAO1 Escherichia coli O157 Listeria monocytogenes serotype 1/2a Staphylococcus aureus Enterococcus faecalis (Streptococcus faecalis) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) 
2021-04-12 | PXD024904 | Pride
Assay library Bacteria Lc-ms/ms 
ProteomicsQuantitative analysis of proteomic changes induced by potential quorum sensing in Haloferax volcanii
Quorum sensing (QS) is a mechanism of intercellular communication that enables microbes to alter gene expression and adapt to the environment. While QS has been extensively studied in bacteria, little is known about cell-cell communication in archaea. We could show that for Haloferax volcanii, the t...
ORGANISM(S): Haloferax volcanii (Halobacterium volcanii) Archaea 
2025-06-17 | PXD059278 | Pride
Archaeal proteome project Ursgal Archaea Haloferax volcanii Label-free quantification Quorum sensing Cell shape 
ProteomicsHuman brain LC-MS/MS - Brain Citrullination Patterns and T Cell Reactivity of Cerebrospinal Fluid-Derived CD4+ T Cells in Multiple Sclerosis
Citrullination as a post-translational modification has been described in a couple of autoimmune diseases like rheumatoid arthritis (RA) and multiples sclerosis (MS). We investigated citrullination brain tissue from MS patients and healthy individuals (HD). The myelin sheath proteins have been the f...
ORGANISM(S): Homo sapiens (Human) 
2019-04-10 | PXD008344 | Pride
Pressure cycle technology (pct) Post-translational modification (mbp) Mass spectrometry Human post mortem brain tissue Hydrophilic interaction liquid chromatography hilic Myelin basic protein Citrullination Multiple sclerosis (ms) Neurodegeneration 
ProteomicsMass spectrometric analysis of proteolytic cleavage related to ArtA and PssA from Haloferax volcanii
The S-layer glycoprotein (SLG) of Haloferax volcanii has been shown to be processed and C-terminally linked to a lipid in an archaeosortase A (ArtA)-dependent manner. A C-terminal tripartite structure including a PGF motif is required for the processing of SLG as well as other substrates (Abdul Hali...
ORGANISM(S): Haloferax volcanii (Halobacterium volcanii) 
2020-05-11 | PXD011050 | Pride
Haloferax volcanii Lipid anchoring Archaeosortase S-layer glycoprotein 
ProteomicsChlamydomonas reinhardtii Mannosidase 1A and Xylosyltransferase1A N-glycosylation LC/MS-MS
We have identified insertional mutants of mannosidase 1A and xylosyltransferase 1A in Chlamydomonas reinhardtii. Mass spectrometric analyses of intact N-glycopeptides revealed that disruption of the genes altered the N-glycan composition of the alga (in single as well as double mutant). In contrast ...
ORGANISM(S): Chlamydomonas reinhardtii 
2018-02-27 | PXD005254 | Pride
Chlamydomonas reinhardtii N-gylcoproteomics Lc-ms/ms 
ProteomicsGlycoproteomic analysis of Haloferax volcanii strains H53, DaglB, and Dagl15
An in-depth glycoproteomic analysis of Haloferax volcanii has been performed, comparing the wildtype H53 with knockout mutants of aglB and agl15. While AglB-dependent glycosylation has been described to occur under standard culture conditions, the Agl15-dependent glycosylation pathway has previously...
ORGANISM(S): Haloferax volcanii (Halobacterium volcanii) 
2021-06-20 | PXD021874 | Pride
Glycoproteomics Glycosylation Archaea Haloferax volcanii 
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