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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 (Human) 
2014-10-20 | PXD001390 | Pride
Proteoannotator 
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 
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
UnknownIntegrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation.
Not available
S-EPMC4762527 | biostudies-literature
ProteomicsNeospora Caninum whole proteome study
MS/MS dataset for proteogenomics study of Neospora Caninum. The dataset was searched against the official v10 gene model from ToxoDB, and the alternate panels of proteins predicted from RNA-SEQ evidences.
ORGANISM(S): Neospora Caninum (strain Liverpool) 
2015-02-09 | PXD000298 | Pride
Proteogenomics Neospora caninum 
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 
ProteomicsLarge scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative endosymbiont C4PR_LIV
The majority of bacterial genomes have high coding efficiencies, but there are an few genomes of the intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic...
ORGANISM(S): Sodalis glossinidius 
2020-05-26 | PXD007068 | Pride
Proteomics Genomics Transcriptomics Proteogenomics 
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