PXD066654
PXD066654 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Spotted hyena lymph node, liver, and lung proteomes |
| Description | Proteomics using Draft Genomes: a Case Study in Spotted Hyena Crocuta crocuta, or spotted hyena, are one of four remaining hyena species, notable for its preference for hunting rather than scavenging. Until 2020, no annotated genome had been published for the species; by 2023, three had been published. These bottom-up proteomes, measured in 2020, were used to evaluate the quality of these three genomes for C. crocuta, establishing that the genome annotation featured by UniProt and NCBI lags behind the alternatives in identification sensitivity. Sample handling and mass spectrometry are detailed in 1330MASS_ANALYTICALREPORT.pdf. Notably, these data were produced with Cys alkylated by MMTS rather than iodoacetamide. The search results come from FragPipe 23, using the "Shao.faa" fasta plus contaminants and decoys. These shotgun proteomes were collected in roughly three sets. The three "Test" experiments (March and July 2020) established the amount of peptides loaded on column and asked how peptide diverse the samples were. The 13 RPLC experiments (August 2020) represented peripheral, head, abdominal, or thoracic lymph nodes (PL, HL, AL, or TL) from three different animals (571, 572, and 575) plus a few liver and lung samples. The 12 "Fraction" RAWs (September 2020) represent ten bRPLC fractions of a head lymph node pool. See the QuaMeter.tsv table for more details. These animals are the same as were used for RNA-Seq in NCBI PRJNA658551. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-07-28 |
| AnnouncementXML | Submission_2025-07-28_05:12:24.710.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | David L. Tabb |
| SpeciesList | scientific name: Crocuta crocuta; common name: spotted hyena; NCBI TaxID: 9678; |
| ModificationList | L-cysteine methyl disulfide; Acetyl |
| Instrument | Q Exactive |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-07-28 04:56:04 | ID requested | |
| ⏵ 1 | 2025-07-28 05:12:25 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: DDA, shotgun, DatasetType:Proteomics |
Contact List
| David L. Tabb | |
|---|---|
| contact affiliation | Stellenbosch University |
| contact email | dtabb@sun.ac.za |
| lab head | |
| David L. Tabb | |
| contact affiliation | University of Groningen |
| contact email | d.l.tabb@rug.nl |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v10/MSV000098657/ |
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