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Proteomics2D-LC/MS/MS analysis of Escherichia coli under optimal growth condition
2D-LC/MS/MS analysis was used to examine the proteome of E. coli O157:H7 strain Sakai during exponential growth under optimal condition (i.e., from 35°C aw 0.993). MS/MS data obtained from each protein sample were processed by the Computational Proteomics Analysis System (CPAS), a web-based system ...
ORGANISM(S): Escherichia coli 
2019-12-04 | PXD000583 | Pride
Optimal growth condition Physiology 2d-lc/ms/ms E. coli 
ProteomicsImproved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline
Fragmentation ion spectral analysis of chemically crosslinked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which...
ORGANISM(S): Bos taurus (Bovine) Saccharomyces cerevisiae (Baker's yeast) 
2023-01-18 | PXD037492 | Pride
Kojak Crosslinking mass spectrometry Proteomics Software tools Protein interaction Peptideprophet Xl-ms Trans-proteomic pipeline Computational proteomics Iprophet 
UnknownOptimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics.
Not available
S-EPMC2040164 | biostudies-literature
ProteomicsHuman plasma LC-MS/MS - Human plasma partitioning with acetonitrile
Human plasma partitioning with acetonitrile at pH 5. Crude plasma, supernatant and pellet fractions obtained after precipitation were analyzed with X!Tandem and SpectraST; assigned with PeptideProphet probabilities were then combined using InterProphet.
ORGANISM(S): Homo sapiens (Human) 
2012-12-05 | PXD000042 | Pride
Human Plasma Organic precipitation Lc-ms/ms 
Proteomics2D-LC/MS/MS analysis of Escherichia coli during exposure to an abrupt temperature downshift
2D-LC/MS/MS analysis was used to examine time-dependent changes in proteome of E. coli O157:H7 strain Sakai upon an abrupt downshift in temperature (i.e., from 35°C to 14°C). Cell cultures were harvested at 30, 90, 160, and 330 min post-temperature downshift. It also should be noted that these time ...
ORGANISM(S): Escherichia coli 
2019-11-25 | PXD000573 | Pride
Physiology Stress response 2d-lc/ms/ms E. coli Cold stress 
UnknownProteome identification of the silkworm middle silk gland.
Not available
S-EPMC4753389 | biostudies-literature
UnknownImproved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.
Not available
S-EPMC10234491 | biostudies-literature
ProteomicsThe Skin Barrier Defects Caused by Keratinocyte-Specific Deletion of ADAM17 or EGFR are Based on Highly Similar Proteome and Degradome Alterations
ADAM17 and EGFR are essential key players for epidermal integrity. Keratinocyte-specific deletion of ADAM17 in mice results in pronounced alterations in terminal differentiation of keratinocytes leading to severe epidermal barrier defects with enhanced transepidermal water loss. Thereby, mice defici...
ORGANISM(S): Mus musculus (Mouse) 
2016-04-20 | PXD002597 | Pride
Proteomics Skin Degradomics 
UnknownMetaLP: An integrative linear programming method for protein inference in metaproteomics.
Not available
S-EPMC9629623 | biostudies-literature
UnknownProteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer.
Not available
S-EPMC3069718 | biostudies-literature
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