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ProteomicsExtensive and accurate benchmarking of DIA acquisition methods and softwares using a complex
In order to compare workflows for acquisition and treatment of proteomic data analyzed in Data Independent Acquisition (DIA) mode, a proteomic standard has been generated by spike-in the 48 human proteins of UPS1 (Sigma) in a whole cell extract of E.coli at 8 different concentrations ranging from 0....
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) 
2021-06-09 | MSV000087597 | MassIVE
ProteomicsEvaluation of iTRAQ and SWATH-MS for the quantification of proteins associated with insulin resistance in human duodenal biopsy samples
Insulin resistance (IR) is associated with increased production of triglyceride-rich lipoproteins of intestinal origin. In order to assess whether insulin resistance affects the proteins involved in lipid metabolism, we used two mass spectrometry based quantitative proteomics techniques to compare t...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
MSV000080194 | MassIVE
ProteomicsFast and accurate bacterial species identification in biological samples using LC-MS/MS mass spectrometry and machine learning (DDA dataset)
We have developed a new strategy for identifying bacterial species in biological samples using specific LC-MS/MS peptidic signatures. In the first training step, deep proteome coverage of bacteria of interest is obtained in Data Independent Acquisition (DIA) mode, followed by the use of machine lear...
ORGANISM(S): Citrobacter Freundii (ncbitaxon:546) Streptococcus Agalactiae 2603v/r (ncbitaxon:208435) Staphylococcus Aureus Subsp. Aureus Nctc 8325 (ncbitaxon:93061) Streptococcus Mitis (ncbitaxon:28037) Klebsiella Oxytoca (ncbitaxon:571) Staphylococcus Epidermidis Atcc 12228 (ncbitaxon:176280) Enterococcus Faecalis V583 (ncbitaxon:226185) Enterobacter Aerogenes Kctc 2190 (ncbitaxon:1028307) Proteus Mirabilis (ncbitaxon:584) Escherichia Coli K-12 (ncbitaxon:83333) Enterobacter Cloacae (ncbitaxon:550) Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 (ncbitaxon:272620) Pseudomonas Aeruginosa Pao1 (ncbitaxon:208964) Staphylococcus Saprophyticus Subsp. Saprophyticus Atcc 15305 (ncbitaxon:342451) Staphylococcus Haemolyticus Jcsc1435 (ncbitaxon:279808) 
2019-05-16 | MSV000083784 | MassIVE
ProteomicsEvaluation of iTRAQ and SWATH-MS for the quantification of proteins associated with insulin resistance in human duodenal biopsy samples
Insulin resistance (IR) is associated with increased production of triglyceride-rich lipoproteins of intestinal origin. In order to assess whether insulin resistance affects the proteins involved in lipid metabolism, we used two mass spectrometry based quantitative proteomics techniques to compare t...
ORGANISM(S): Homo sapiens (Human) 
2015-08-26 | PXD001506 | Pride
Human duodenum Swath-ms Quantitative proteomics Itraq 
ProteomicsFast and accurate bacterial species identification in biological samples using LC-MS/MS mass spectrometry and machine learning (DIA dataset)
We have developed a new strategy for identifying bacterial species in biological samples using specific LC-MS/MS peptidic signatures. In the first training step, deep proteome coverage of bacteria of interest is obtained in Data Independent Acquisition (DIA) mode, followed by the use of machine lear...
ORGANISM(S): Citrobacter Freundii (ncbitaxon:546) Streptococcus Agalactiae 2603v/r (ncbitaxon:208435) Staphylococcus Aureus Subsp. Aureus Nctc 8325 (ncbitaxon:93061) Streptococcus Mitis (ncbitaxon:28037) Klebsiella Oxytoca (ncbitaxon:571) Staphylococcus Epidermidis Atcc 12228 (ncbitaxon:176280) Enterococcus Faecalis V583 (ncbitaxon:226185) Enterobacter Aerogenes Kctc 2190 (ncbitaxon:1028307) Proteus Mirabilis (ncbitaxon:584) Escherichia Coli K-12 (ncbitaxon:83333) Enterobacter Cloacae (ncbitaxon:550) Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 (ncbitaxon:272620) Pseudomonas Aeruginosa Pao1 (ncbitaxon:208964) Staphylococcus Saprophyticus Subsp. Saprophyticus Atcc 15305 (ncbitaxon:342451) Staphylococcus Haemolyticus Jcsc1435 (ncbitaxon:279808) 
2019-05-16 | MSV000083793 | MassIVE
TranscriptomicsGene expression profile of calcified and normal tricuspid aortic valves by RNA sequencing.
Purpose: Calcific aortic valve stenosis (AS) is a fatal disease with currently no medical therapy. Some genes were associated with AS, but the genetic architecture of the disease has yet to be discovered. The objective of this study was to combine genome-wide association studies (GWAS) and gene expr...
ORGANISM(S): Homo sapiens 
2015-12-09 | E-GEOD-55492 | biostudies-arrayexpress
TranscriptomicsIntegration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia
B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation s...
ORGANISM(S): Homo sapiens 
2013-06-04 | E-GEOD-38235 | biostudies-arrayexpress
ProteomicsExtracellular Glutathione Peroxidase 3 GPx3 Levels are Markedly Reduced in Children Affected with Konzo an Irreversible Spastic Paralysis Associated with Food Poisoning
Konzo, a neglected paralytic neurological disease associated with food (cassava) poisoning, affects the world poorest children and women of childbearing ages across regions of sub Saharan Africa, with the Democratic Republic of the Congo having the largest case burden. The primary risk factors for d...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-02-20 | MSV000094134 | MassIVE
ProteomicsIntegrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation
We performed proteomics on naturally infested green ash (F. pennsylvanica) trees at low and high levels of emerald ash borer (A. planipennis) infestation. Our integrative analysis of the RNA-Seq and proteomics data identified 14 proteins and 4 transcripts that contribute most to the difference betw...
ORGANISM(S): Fraxinus Pennsylvanica (ncbitaxon:56036) 
MSV000090439 | MassIVE
ProteomicsMEF2A, MEF2C, and MEF2D Interactomes in Mouse MA-10 Leydig Cells
In steroidogenic Leydig cells, MEF2A, MEF2C, and MEF2D are key regulators of genes involved in steroid hormone synthesis, reproductive function, and oxidative stress defense. Here we used TurboID proximity-mediated biotinylation to map the protein-protein interaction networks of MEF2A, MEF2C, and ME...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2024-11-15 | MSV000096432 | MassIVE
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