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MetabolomicsMetabolome analysis via an HPLC-ESI-MS-based experimental and computational pipeline for chronic nephron toxicity profiling
Untargeted metabolomics has the potential to improve the predictivity of in vitro toxicity models and therefore may aid the reduction of expensive and laborious animal models. Here we describe a chronic nephrotoxicity study conducted on a human renal proximal tubular epithelial cell line (RPTEC/TERT...
2015-09-07 | MTBLS140 | MetaboLights
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 
ProteomicsPTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
Analysis of synthetic peptide reference datasets to demonstrate the performance of PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization co...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-01-10 | MSV000096828 | MassIVE
ProteomicsPTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
Analysis of synthetic peptide reference datasets to demonstrate the performance of PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization co...
ORGANISM(S): Homo sapiens (Human) 
2019-07-18 | PXD013210 | Pride
Site localization Synthetic phospho-peptides Human Lc-ms/ms 
UnknownStPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline.
Not available
S-EPMC5891225 | biostudies-literature
UnknownProcessing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.
Not available
S-EPMC4350034 | biostudies-literature
UnknownPTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline.
Not available
S-EPMC6898736 | 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
ProteomicsEts-2 propagates IL-6 trans-signaling mediated osteoclast-like changes in human rheumatoid arthritis synovial fibroblast
Interleukin-6 (IL-6) plays an important role in progressive bone loss in rheumatoid arthritis (RA). However, the molecular mechanisms through which IL-6 propels RA synovial fibroblasts (RASFs) to contribute to bone loss are not fully understood. In the present study, we investigated the effects of I...
ORGANISM(S): Homo sapiens (Human) 
2021-11-02 | PXD028374 | Pride
Interleukin 6 Osteoclast Synovial fibroblast Rheumatoid arthritis 
ProteomicsDirect glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced association tandem mass spectrometry and predicted spectral library searching
Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a novel computationa...
ORGANISM(S): Homo sapiens (Human) 
2016-08-17 | PXD002803 | Pride
Glycopeptide Lc-msms 
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