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ProteomicsGeneration of ENSEMBL-based proteogenomics databases boost the identification of novel peptides - Mouse dataset
A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, a...
ORGANISM(S): Mus musculus (Mouse) 
2021-10-26 | PXD029362 | Pride
Mouse Mice 
ProteomicsGeneration of ENSEMBL-based proteogenomics databases boost the identification of novel peptides
A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, an...
ORGANISM(S): Homo sapiens (Human) 
2021-10-26 | PXD029360 | Pride
Ensembl Reanalysis Proteogenomics 
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): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2016-09-27 | PXD002952 | Pride
Lfqbench Lfq Swath-ms Benchmark 
ProteomicsAn AI-ready phosphorylation meta-analysis for Saccharomyces cerevisiae.
We, the PTMeXchange Consortium, present a meta-analysis of eight high-quality data sets to map 56,694 phosphosites in brewer's yeast (Saccharomyces cerevisiae) using strict control for false identifications. Each site has been classified into the Gold-Silver-Bronze (GSB) categories depending on the ...
ORGANISM(S): Saccharomyces cerevisiae 
2025-12-16 | PXD071918 | Pride
ProteomicsPhosphorylation in the Plasmodium falciparum proteome: A meta-analysis of publicly available data sets
Malaria is a deadly disease caused by Apicomplexan parasites of the Plasmodium genus. Several species of the Plasmodium genus are known to be infectious to human, of which P. falciparum is the deadliest. Post-translational modifications (PTMs) of proteins coordinate cell signalling and hence, regula...
ORGANISM(S): Plasmodium falciparum 
2023-11-22 | PXD046874 | Pride
Phosphoproteomics Ptmexchange Flr Public data Reanalysis 
ProteomicsA meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome
Abstract We have re-analysed publicly available mass spectrometry (MS) data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we have identified, 15522 phosphosites on Serine, Threonine and Tyrosine residues on rice proteins. The data has been loaded into UniProtKB, enabling...
ORGANISM(S): Oryza sativa (Rice) 
2023-11-08 | PXD046188 | Pride
Phosphoproteomics Ptmexchange Flr Public data Reanalysis 
ProteomicsMaxDIA enables highly sensitive and accurate library-based and library-free data-independent acquisition proteomics (DIA data)
MaxDIA is a universal platform for analyzing data-independent acquisition proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves cutting-edge proteome coverage with significantly better coefficients of variation in protein quantification than other softwa...
ORGANISM(S): Candida albicans (Yeast) Homo sapiens (Human) Escherichia coli 
2021-07-09 | PXD022589 | Pride
Maxquant Benchmark 
ProteomicsMaxDIA enables highly sensitive and accurate library-based and library-free data-independent acquisition proteomics (DDA data)
MaxDIA is a universal platform for analyzing data-independent acquisition proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves cutting-edge proteome coverage with significantly better coefficients of variation in protein quantification than other softwa...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2021-07-09 | PXD022582 | Pride
Maxquant Benchmark 
ProteomicsA comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics
A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics using SCIEX TripleTOF5600 and 6600+, Orbitrap QE-HFX, Waters Synapt GS-Si and Synapt XS and Bruker timsTOF Pro.
ORGANISM(S): Candida albicans (Yeast) Homo sapiens (Human) Escherichia coli 
2022-02-14 | PXD028735 | Pride
Swath Dia Benchmark 
ProteomicsA protein standard that emulates homology for the characterization of protein inference algorithms
A natural way to benchmark the performance of an analytical experimental setup is to use samples of known content, and see to what degree one can correctly infer the content of such a sample from the data. For shotgun proteomics, one of the inherent problems of interpreting data is that the measured...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) 
MSV000084315 | MassIVE
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