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UnknownA software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS.
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S-EPMC3437041 | biostudies-literature
ProteomicsAssessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance
Proteome wide protein quantification has become facile in the last years supported by label-free discovery proteomics approaches and powerful, easy to use software. We set out to independently evaluate this highly peptide centric technology focusing on the performance of some of the currently most p...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2017-03-07 | PXD004025 | Pride
Arabidopsis Label-free Protein inference Progenesis qip Shotgun proteomics Maxquant Epigenetics Scaffold 
MetabolomicsBioconversion properties and anti-hyperuricemic capacity of urate-lowering probiotic fermented Aronia melanocarpa (black chokeberry) beverage

Hyperuricemia (HUA) is a global metabolic disorder characterized by abnormally elevated serum uric acid (UA) (SUA) level, and this study aimed to design a functional fermented beverage based on the urate-lowering probiotic Lactobacillus paracasei N1115 (LP) and Aronia melanocarpa (black chokeberr...

2025-11-28 | MTBLS13414 | MetaboLights
ProteomicsBartonella henselae mutant label-free analysis
We prepared 6 different mutants of the VirB proteins in B. henselae in triplicates and run 2h gradient 1D-LC-MS analysis. Relative quantification was carried out by the Progenesis LC-MS software
ORGANISM(S): Bartonella henselae (strain ATCC 49882 / Houston 1) (Rochalimaea henselae) 
2016-06-21 | PXD000180 | Pride
Label-free quantification B. henselae 
ProteomicsEPAC1 knockout mouse effects in platelets and plasma
ABSTRACT FOR BOTH PLASMA AND PLATELET-LYSATE In this article we describe the involvement of exchange factor activated by cAMP 1 (Epac1) in hemostasis and platelet activation. We have used plasma and platelet-lysate from EPAC1 knockout mice and wild-type control mice in label-free proteomics with an ...
ORGANISM(S): Mus musculus (Mouse) 
2017-07-25 | PXD000282 | Pride
Epac1 knockout Platelets Lc-ms Plasma Label-free 
ProteomicsAnalysis of the ubiquitinated peptides using the yeast Rpt2-normal, G2A and G2delta strains
Ubiquitinated peptides (KGG peptides) purified from the yeast strains with or without mutation on the N-myristoylation site of the proteasome Rpt2 subunit were analyzed by an LTQ-Orbitrap Velos. The MS data was analyzed by the Progenesis LC-MS software.
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2017-08-25 | PXD002274 | Pride
Yeast Proteasome Ubiquitin Lc-ms/ms 
MetabolomicsFlavonoid pathway intermediates implicate UVR8 in functions beyond canonical UV-B signaling

Plants integrate light signals to regulate development and produce protective compounds such as flavonoids under excessive light stress. While these metabolites protect against light damage, their roles in modulating photoreceptor responses remain unclear. Here we show that naringenin chalcone (N...

2025-07-30 | MTBLS12792 | MetaboLights
ProteomicsHuman keratinocytes HaCaT LC-MS/MS
Triton X-100 has been used as a model substance to study the effects of irritants on the skin. HaCaT human keratinocyte cell line were treated with a non-cytotoxic dose of Triton X-100, as determined by the MTT assay and microscopically examination) for 48 h. The altered abundance of proteins from H...
ORGANISM(S): Homo sapiens (Human) 
2017-11-03 | PXD007776 | Pride
Hacat keratinocytes Shotgun proteomics Exposure Triton x-100 
MetabolomicsNHE gene knockdown in the Chinese mitten crab
Metabolomic analysis of anadromous juvenile crabs at different salinities following NHE gene knockdown
2026-04-22 | MTBLS14342 | MetaboLights
Proteomicscomparative proteomic analysis without a label based on the technology of tandem HPLC - MS/MS
The relative differences between post-translational modifications (PTM) of proteins in blood plasma samples of patients with cerebral ischemia (CI) and healthy people were investigated on the basis of the method of comparative proteomic analysis without a label based on the technology of tandem HPLC...
ORGANISM(S): Homo sapiens (Human) 
2019-12-04 | PXD012974 | Pride
Liquid chromatography and mass spectrometry Post-translational modifications of proteins Cerebral ischemia Blood plasma proteome Orbitrap 
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