Sort   by:  
 Page size 
ProteomicsProteogenomic analysis of Toxoplasma gondii (comparing genome releases 6 and 10) to demonstrate the performance of the ProteoAnnotator software
Testing the performance of the ProteoAnnotator software via comparing analysis of annotating the Toxoplasma gondii gene models 6 and 10
ORGANISM(S): Toxoplasma gondii ME49 
2014-10-20 | PXD001042 | Pride
Proteogenomics Proteoannotator Annotation Toxoplasma gondii Orbitrap 
ProteomicsImprovements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics data sets
We have performed a Proteogenomics meta-analysis of data sets deposited in ProteomeXchange: PXD000265, PXD000313, PXD000923, PXD001030, PXD001058, PXD002291, PXD002739, PXD002740 and PXD003156 and using 29 RNA-Seq data sets on rice (Oryza sativa). We created a search database comprising translated r...
ORGANISM(S): Oryza sativa (Rice) 
2018-10-30 | PXD008960 | Pride
Rice Proteogenomics Proteomics Rna-seq Big data analysis 
ProteomicsA landscape analysis of human SUMOylation: A comprehensive meta-analysis of publicly available datasets
SUMOylation is an important but understudied post-translational modification (PTM) linked to diverse physiological and pathological processes. Various laboratories have developed protocols for identifying SUMOylation target sites using SUMO enrichment followed by mass spectrometry. As part of the PT...
ORGANISM(S): Homo sapiens 
2025-12-16 | PXD068489 | Pride
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
ProteomicsToxoplsama Gondii whole proteome study
MS/MS dataset for proteogenomics study of Toxoplasma gondii. The dataset was searched against the official v9 gene model from ToxoDB, and the alternate panels of proteins predicted from RNA-SEQ evidences.
ORGANISM(S): Toxoplasma gondii RH 
2015-02-09 | PXD000297 | Pride
Toxoplasma Proteogenomics 
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 
ProteomicsRe-analysis of: ‘CSF proteome mapping: Human cerebrospinal fluid LC-MS/MS, Part 2’ (PXD000652) to demonstrate the ProteoAnnotator software for mapping identifications to Ensembl genomes
We have performed a re-analysis of PXD000652 - a human proteome CSF fluid sample, originally queried versus UniProt. We have used our ProteoAnnotator package to re-search the data against Ensembl Human build 76 to demonstrate the capability of the pipeline to perform genome mapping on a large scale.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
MSV000080193 | MassIVE
ProteomicsA method for independent estimation of false localisation rate for phosphoproteomics
Phosphoproteomics methods are commonly employed in labs to identify and quantify the sites of phosphorylation on proteins. In recent years, various software tools have been developed, incorporating scores or statistics related to whether a given phosphosite has been correctly identified, or to estim...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) 
2022-06-09 | PXD028840 | Pride
False localisation Phosphorylation 
ProteomicsPputida - Whole organism, NSAF (Lidburyetal,environmicrobiol,2016)
abundance based on NSAF, Interaction consistency score: 12.3, Coverage: 38
ORGANISM(S): 160488 
2016-00-00 | 1991256584 | PAXDB
Sort   by:  
 Page size