⮝ Full datasets listing
PXD082857-1
PXD082857 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Proteomics of ZFC3H1 depletion in HEK293T cells |
| Description | HEK293T cells were infected with either one of two scramble/non-targeting sgRNAs or one of two ZFC3H1-targeting sgRNAs (three biological replicates per sgRNA). These cells were harvested 9 days after infection. Twenty ug of each sample was adjusted to 5% SDS, reduced and alkylated followed by trypsin digestion using an S-trap. After lyophilization and reconstitution of the sample in 40 ul, 2 ul of each was analyzed by LC-MS/MS using a Evosep One LC coupled to a Thermo Orbitrap Astral. Each sample was analyzed in singlicate and in a block-randomized order and interspersed with replicates of a study pool QC (SPQC) sample. The Evosep used a 30 sample-per-day method with a Pepsep 15 cm x 150 um column (1.5 um particle size) with a PepSep Sprayer and stainless steel (30 um) emitter. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r=240,000 (@ m/z 200) full MS scan every 0.6 s from m/z 380-980 with an AGC target of 500%. DIA MS/MS scans were acquired in the Astral analyzer using fixed windows of 4 m/z from m/z 380, target AGC of 500% and max fill time of 6 ms. HCD collision energy setting of 28% was used for all MS2 scans. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-08-19 |
| AnnouncementXML | Submission_2026-08-19_19:15:16.977.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Matt Foster |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Acetyl; Carbamidomethyl |
| Instrument | Orbitrap Astral |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-08-19 12:41:23 | ID requested | |
| ⏵ 1 | 2026-08-19 19:15:17 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: PAXT, ZFC3H1, RNA exosome, codon bias, DatasetType:Proteomics |
Contact List
| Christopher Counter | |
|---|---|
| contact affiliation | Duke University Medical Center |
| contact email | chris.counter@duke.edu |
| lab head | |
| Matt Foster | |
| contact affiliation | Duke University |
| contact email | mwfoster@duke.edu |
| 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/v14/MSV000102919/ |
