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ProteomicsNickel Binding- and Histidine-Rich Proteins of Helicobacter species
The files in this archive examine six species within the genus Helicobacter to assay their histidine-rich proteins. They correspond to the manuscript "Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species" by Frederic Fischer, Egor Vorontsov, Eve...
ORGANISM(S): Helicobacter Felis (ncbitaxon:214) Helicobacter Bizzozeronii (ncbitaxon:56877) Helicobacter Pylori (ncbitaxon:210) Helicobacter Acinonychis (ncbitaxon:212) Helicobacter Mustelae (ncbitaxon:217) Helicobacter Hepaticus (ncbitaxon:32025) 
2022-03-23 | MSV000089106 | MassIVE
ProteomicsGlobal protein expression profiles of laboratory isolated mutants of E. coli K12, MG1655
Resistance to the antibiotic mecillinam in Escherichia coli can be conferred by mutations in over 100 genes. In this study we compared the global protein expression levels in a number of mecillinam resistant mutants originating from E. coli MG1655 to the levels in the parental strain.
ORGANISM(S): Escherichia coli 
2019-07-29 | PXD007647 | Pride
Escherichia coli Tmt Q exactive Tandem mass tag Microbiology Antibiotic resistance Orbitrap fusion 
ProteomicsImpact of Age and Sex on Plasma Proteome Changes in Mice upon Radiation Exposure
The aim of this project is to assess the impact that age and sex have as parameters for biomarker discovery in radiation research using high-throughput proteomics.
ORGANISM(S): Mus musculus (Mouse) 
2022-05-10 | PXD015859 | Pride
Plasma Radiation Mus musculus Tmt Sex Tandem-mass tag Mouse Age Orbitrap fusion 
ProteomicsA bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function
One key concept in the evolution of new functions is the ability of enzymes to perform promiscuous side-reactions that serve as a source of novelty that may become beneficial under certain conditions. Here, we identify a mechanism where a bacteriophage-encoded enzyme introduces novelty by inducing e...
ORGANISM(S): Escherichia coli 
2018-05-11 | PXD005236 | Pride
Tmt Escherichia coli Antibiotic resistance Orbitrap fusion 
ProteomicsSulfolobus islandicus PTM and quantitative study using bottom-up proteomics
Protein posttranslational methylation and acetylation have been reported to occur in archaea, including the genus Sulfolobus, but have never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modifications are the chromatin proteins that have been describe...
ORGANISM(S): Sulfolobus islandicus LAL14/1 Escherichia coli 
2016-09-13 | PXD004179 | Pride
Methylation Archaea Sulfolobus islandicus Label-free quantitation Orbitrap fusion Posttranslational modification 
ProteomicsTMT-based Study of Gene Expression Changes in Escherichia coli in Presence of Plasmids
The plasmids introduced into the E. coli cells affect the expression of chromosomal genes. Therefore we aimed at comparing the protein expression profiles of a strain not containing any plasmid with strains that do carry plasmids.
ORGANISM(S): Escherichia coli 
2021-12-14 | PXD014039 | Pride
Escherichia coli Tmt Tandem mass tag Plasmid 
ProteomicsIdentification of a chondroitin sulfate linkage region trisaccharide
Here, using LC-MS/MS, we describe for the first time a linkage region trisaccharide comprising [-GlcUA-Gal-Xyl-O-] as an alternative point of entry for glycosaminoglycan (GAG) biosynthesis. The trisaccharide was identified in the proteoglycan bikunin from urine of human healthy donors present as a d...
ORGANISM(S): Homo sapiens (Human) 
2019-02-25 | PXD011855 | Pride
Glycosaminoglycan Lc-ms Chondroitin sulfate Hcd Negative ionisation mode Orbitrap Bikunin 
ProteomicsGlycosaminoglycan Domain Mapping of cellular chondroitin/dermatan sulfates
Here we report a simple and versatile approach for domain mapping of complex mixtures of glycosaminoglycans (GAGs), GAGDoMa. The approach is based on orthogonal enzymatic depolymerization of the GAGs, generating internal oligosaccharide, non-reducing end, and linkage region GAG domains, nanoflow rev...
ORGANISM(S): Homo sapiens (Human) 
2020-02-18 | PXD014504 | Pride
Higher-energy collision dissociation Gags Glycosaminoglycans Hcd Orbitrap elite Glycomics Negative ionisation mode Ion-pairing reversed-phase chromatography Dermatan sulfate Chondroitin sulfate 
ProteomicsQuantifying gene expression control by growth and metabolism reveals distinct regulation of central carbon metabolism genes in yeast
Here we quantitatively describe the influence of cell growth rate and amino acid metabolic context on gene expression in the eukaryal model organism Saccharomyces cerevisiae. We show that growth rate and metabolic cues regulate ~70% of the yeast transcriptome and proteome, thereby exerting gene expr...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-03-15 | PXD021218 | Pride
Tmt Yeast Tandem mass tag Saccharomyces cerevisiae Lfq Label-free quantification Systems biology Orbitrap fusion 
ProteomicsSulfolobus islandicus top-down LC-MSMS
Protein posttranslational methylation and acetylations have been reported to occur in archaea, including members of the genus Sulfolobus, but have not been characterized on a proteome-wide scale. Sulfolobus chromatin proteins are known to be methylated and acetylated on lysine side chains, resemblin...
ORGANISM(S): Sulfolobus islandicus LAL14/1 
2016-09-13 | PXD003074 | Pride
Archaea Top-down Lc-msms Orbitrap fusion 
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