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ProteomicsMS1Connect: a mass spectrometry run similarity measure
Researchers may be interested in finding proteomics runs, which have been deposited into online repositories, that are similar to their own data. However, it is difficult to measure the similarity of a pair of proteomics runs. Here, we present a new method, MS1Connect, that only uses intact peptide ...
ORGANISM(S): Porphyrobacter sp. WLSH-3 Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 Nicotiana benthamiana Bacillus thuringiensis Escherichia coli Bacillus cereus Bacillus thuringiensis str. Al Hakam 
2023-01-05 | PXD027791 | Pride
Bacteria Similarity 
ProteomicsAccurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant
The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are reDR control strategies ...
ORGANISM(S): Ricinus communis Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-06-17 | PXD022778 | Pride
Ups1 Ricin Yeast Castor Human 
ProteomicsCombining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2
This project reanalzyes data from 4 other projects. Information about the samples can be found in the following four publications. The four samples used in this study include a ocean metaproteome sample, a human sample, a E. coli sample, and a Plamodium falciparum sample. B. N. Pease, E. L. Huttli...
ORGANISM(S): Homo sapiens (Human) Plasmodium falciparum (isolate 3D7) Escherichia coli 
2018-09-19 | PXD009265 | Pride
E. coli Score function Ocean Human Plasmodium 
UnknownReal-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics.
Not available
S-EPMC11554524 | biostudies-literature
ProteomicsRNA MS2-tag based affinity method was used to purify 3' processing factors associated with intronic PAS processing
three copies of the MS2 hairpin were fused to the intronic PAS of the nr3c1 gene. To make a negative control RNA substrate, the core hexamer AAUAAA within PAS was mutated to AACAAA. Subsequently, the RNA substrate was incubated with HeLa NE, and the mRNA 3' processing complex was purified using an M...
ORGANISM(S): Homo Sapiens 
2023-02-27 | PXD040405 |
ProteomicsQuantitative Proteomic Study Unmasks Fibrinogen Pathway in Polycystic Liver Disease
(1) Background: Polycystic liver disease (PLD) is a heterogeneous group of congenital disorders characterized by bile duct dilatation and cyst development derived from cholangiocytes. Nevertheless, the cystogenesis mechanism is currently unknown and the PLD treatment is limited to liver transplantat...
ORGANISM(S): Mus musculus (Mouse) 
2022-04-04 | PXD031253 | Pride
Pld  swath  quantitative proteomics  therapeutic targets 
ProteomicsDeep quantitative proteomics of North American Pacific coast star tunicate
The first proteomics analysis of a colonial tunicate (Botryllus schlosseri) was carried out to support development of a DIA assay library and quantitative proteomics for this species. Deep proteome coverage (up to 4930 protein groups and 20,984 unique peptides in a single sample) was achieved, which...
ORGANISM(S): Botryllus Schlosseri 
2024-02-29 | PXD043046 | panorama
TranscriptomicsGene networks associated with conditional fear in mice identified using a systems genetics approach
To uncover genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and genotype information,...
ORGANISM(S): Mus musculus 
2011-03-15 | E-GEOD-26500 | biostudies-arrayexpress
UnknownROBO4 variants predispose individuals to bicuspid aortic valve and thoracic aortic aneurysm.
Not available
S-EPMC6309588 | biostudies-literature
TranscriptomicsCircadian patterns of gene expression in the human brain and disruption in major depressive disorder
A cardinal symptom of Major Depressive Disorder (MDD) is the disruption of circadian patterns. Yet, to date, there is no direct evidence of circadian clock dysregulation in the brains of MDD patients. Circadian rhythmicity of gene expression has been observed in animals and peripheral human tissues,...
ORGANISM(S): Homo sapiens 
2013-04-20 | E-GEOD-45642 | biostudies-arrayexpress
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