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MetabolomicsAutomated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data (Plasma)

Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require autom...

2015-12-16 | MTBLS234 | MetaboLights
MetabolomicsAutomated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data (Simulated)

Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require autom...

2015-12-16 | MTBLS235 | MetaboLights
ProteomicsLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2017-04-27 | MSV000081024 | MassIVE
ProteomicsSurfactant-assisted one-pot sample preparation for label-free single-cell proteomics
Large numbers of cells are generally required for quantitative global proteome profiling due to the significant surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible...
ORGANISM(S): Homo Sapiens 
2021-03-11 | PXD022827 | panorama
ProteomicsBlack pepper proteome - Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem
In this study, we have evaluated the proteomic changes that occur in Piper nigrum L.(black pepper) after infection by the pathogen Phytophthora capsici. We report novel leaf proteins from black pepper identified by an integrated transcriptome-assisted label-free quantitative proteomics pipeline. Sev...
ORGANISM(S): Piper nigrum 
2016-07-07 | PXD003887 | Pride
Plgs Label-free quantitative proteomics Piper nigrum 
ProteomicsLabel-free quantitative proteome analysis reveals the underlying mechanisms of grain nuclear proteins involved in wheat water-deficit response
In this study, we performed the first large-scale nuclear proteome analysis of wheat developing grains under water deficit by label-free based quantitative proteomic approach.
ORGANISM(S): Triticum aestivum (Wheat) 
2022-02-16 | PXD021315 | Pride
Water deficit Nuclear proteome Developing grains Wheat Label-free quantitation. 
Proteomics4D Label-Free Quantitative N-Glycoproteomic Profiling of 6 Human HCC Cell Samples
4D Label-Free Quantitative N-Glycoproteomic Profiling of 6 Human HCC Cell Samples
ORGANISM(S): Homo sapiens (Human) 
2026-06-11 | PXD068829 | Pride
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ProteomicsComparative analysis of label-free and 8-plex iTRAQ approach for quantitative tissue proteomic analysis
MS-based approaches have been successfully utilized for the comprehensive characterization of the cell proteome. However, in the case of quantitative proteomics the open question still remains, which quantification method is more suitable for identification of proteins with the altered abundance, pa...
ORGANISM(S): Homo sapiens (Human) 
2015-09-09 | PXD002170 | Pride
Lc-ms/ms Bladder cancer Tissue proteomics Label-free Itraq 
ProteomicsLabel-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling
Label-free quantification is a powerful method for studying cellular protein phosphorylation dynamics. However, whether current data normalization methods achieve sufficient accuracy has not been examined systematically. Here, we demonstrate that a large uni-directional shift in the phosphopeptide ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080775 | MassIVE
Proteomics4D Label-Free Quantitative Phosphoproteomics of 12 Cell Samples (3 Groups with 4 Replicates Each)
4D Label-Free Quantitative Phosphoproteomics of 12 Cell Samples (3 Groups with 4 Replicates Each)
ORGANISM(S): Homo sapiens (Human) 
2026-06-11 | PXD074380 | Pride
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