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UnknownSipros Ensemble improves database searching and filtering for complex metaproteomics.
Not available
S-EPMC6192206 | biostudies-literature
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 
ProteomicsErythrocyte Proteome & Terminome
Proteins and protein N termini were isolated and enriched from human erythrocytes following the TAILS procedure with heavy dimethyl labeling of free N-termini (Kleifeld et al. Nat Biothech 2010). Following LC-MS/MS analysis on a Thermo Orbitrap XL spectra were matched using Mascot, X!Tandem and MSGF...
ORGANISM(S): Homo sapiens (Human) 
2014-02-24 | PXD000434 | Pride
Human Red blood cell Acetylation N termini Terminus Rbc Erythrocyte 
UnknownAutomated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet.
Not available
S-EPMC4424409 | 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
UnknownData Independent Acquisition analysis in ProHits 4.0.
Not available
S-EPMC5079801 | biostudies-literature
UnknownDeep learning for peptide identification from metaproteomics datasets.
Not available
S-EPMC8435027 | biostudies-literature
ProteomicsTime-resolved substrate degradomics
20110318_GluC: Cell culture supernatants from Balb/c 3T3 mouse fibroblasts that had been incubated with the endoproteinase GluC (Staphylococcus aureus protease V8) as test protease for 1, 2, 4, 8, and 16 hours or buffer alone (0, 12, and 16 hours controls) were subjected to 8plex-iTRAQ-TAILS analys...
ORGANISM(S): Mus musculus (Mouse) 
2013-12-13 | PXD000503 | Pride
Protease 8plex-itraq Tails Kinetics Mmp 
ProteomicsMycobacterium tuberculosis under starvation
Mycobacterium tuberculosis was grown in Middlebrook 7H9 medium supplemented with 0.4% glycerol, 0.085% NaCL, 0.5% BSA and 0.05% Tyloxapol in roller bottle culture (2 rpm at 37°C). To induce starvation, exponentially growing bacteria were washed and resuspended in PBS supplemented with 0.025% Tyloxap...
ORGANISM(S): Mycobacterium tuberculosis H37Rv 
2013-11-22 | PXD000483 | Pride
Mycobacterium tuberculosis Starvation Dda 
ProteomicsNoordermeer_Shieldin_2018
This dataset consists of 31 raw MS files and associated peak lists and result files, acquired on Thermo Velos Orbitrap, Orbitrap Elite and AB SCIEX TripleTOF 6600 mass spectrometers operated in DDA mode. Samples were processed by Zhen-Yuan Lin. Table 1 describes the composition of this dataset Ta...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-03-25 | MSV000082207 | MassIVE
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