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UnknownOpenMS WebApps: Building User-Friendly Solutions for MS Analysis.
Not available
S-EPMC11811998 | biostudies-literature
ProteomicsFeatureFinderIdentification (OpenMS) analysis of the iPRG-2015 dataset
Benchmark of FeatureFinderIdentification (FFId), a targeted feature detection algorithm for use in label-free quantification, developed in the OpenMS software framework. The dataset used for the evaluation comes from the iPRG-2015 study ("Differential abundance analysis in label-free quantitative pr...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2017-07-07 | PXD006336 | Pride
Iprg-2015 Label-free quantification Feature detection Benchmark Shotgun proteomics 
ProteomicsQuantitation Analysis using OpenMS of iPRG2015: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments
The 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results. The study used LC–tandem mass spectra acquired from a controlled mixture, and made ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-09-10 | PXD010981 | Pride
Openms Label-free Benchmark Iprg2015 Iprg study Reference dataset 
UnknownDDASSQ: An open-source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform.
Not available
S-EPMC8459258 | biostudies-literature
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
Proteomicsyeast membrane proteomics using Leu3 labelling
The yeast signal peptide peptidase homologue Ypf1 functionally interacts with the ER-associated degradation (ERAD) factors Dfm1 and Doa10 to control the abundance of the zinc transporter Zrt1. Here we report that Ctr1 is another substrate for this degradation mechanism with deletion of Ypf1 leading ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2016-04-12 | PXD003052 | Pride
Proteomics Erad Leu3 labelling Yeast Membrane 
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
ProteomicsA dataset for training/testing machine learning models of peptide feature detection: Human HELA LC-MSMS
We introduce MSTracer, a tool for peptide feature detection from MS1, which incorporates a machine-learning-combined scoring function based on peptide isotopic distribution and peptide intensity shape on the LC-MS map. By using Support Vector Regression (SVR), the quality of detected peptide feature...
ORGANISM(S): Homo sapiens (Human) 
2021-06-18 | PXD022287 | Pride
Human Lc-ms/ms 
ProteomicsMS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA
The field of epitranscriptomics is growing in importance, with chemical modification of RNA being associated with a wide variety of biological phenomena. Mass spectrometry (MS) enables the identification of modified RNA residues within their sequence contexts, by using analogous approaches to shotgu...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-03-31 | PXD016308 | Pride
5-methylcytidine Rna Epitranscriptomics Lncrna M5c Nme1 
ProteomicsMS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA
The field of epitranscriptomics is growing in importance, with chemical modification of RNA being associated with a wide variety of biological phenomena. Mass spectrometry (MS) enables the identification of modified RNA residues within their sequence contexts, by using analogous approaches to shotgu...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-12-31 | PXD012095 | Pride
5-methylcytidine Rna Epitranscriptomics Lncrna M5c Nme1 
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