⮝ Full datasets listing
PXD082280-1
PXD082280 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Crosslinking mass spectrometry analysis of N-terminally Halo-tagged C16orf87 transiently expressed in Flp-In-293 cells |
| Description | Halo-C16orf87 Affinity Purification. Protein extracts were incubated with 200 ul Magne HaloTag bead slurry and crosslinked with disuccinimidyl sulfoxide (DSSO, Cayman Chemical Company) MS-cleavable crosslinker. DSSO was added to samples while the proteins were immobilized on beads to a final concentration of 5 mM. Samples were incubated at room temperature for 40 min. Reactions were quenched with the addition of NH4CO3 to a final concentration of 50 mM and samples were incubated an additional 15 min. Bound proteins were eluted by on-beads digestion with AcTEV Protease (Invitrogen) overnight at 25C. Crosslinking Mass Spectrometry and Data Analysis. Digested peptides were analyzed with an Orbitrap Fusion Lumos (Thermo Fisher) coupled to a Dionex U3000 HPLC using previously described data acquisition settings. For each .RAW file, the XlinkX node in Proteome Discoverer v2.4 was used to identify MS2 fragmentation scans with reporter ions characteristic of DSSO crosslinked peptides. Peak lists were searched against a human proteome database (Genome Reference Consortium Human Build 38 patch release 13) containing 44519 unique protein sequences, 426 of which were contaminant proteins. The database was searched for fully tryptic peptides, allowing for a maximum of 2 missed cleavages and a minimum peptide length of 5 amino acids. Precursor mass tolerance, FTMS fragment mass tolerance, and ITMS Fragment tolerance, were set to 10 ppm, 20 ppm, and 0.5 Da, respectively. Xlink Validator FDR threshold was set to 0.01. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-08-06 |
| AnnouncementXML | Submission_2026-08-06_11:01:19.886.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Stowers Proteomics |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; unknown modification; unknown modification |
| Instrument | Orbitrap Fusion Lumos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-08-06 10:51:52 | ID requested | |
| ⏵ 1 | 2026-08-06 11:01:20 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Histone Deacetylase, Crosslinking Mass Spectrometry, Integrative Structural Modeling, DatasetType:Proteomics |
Contact List
| Laurence Florens | |
|---|---|
| contact affiliation | The Stowers Institute for Medical Research |
| contact email | laf@stowers.org |
| lab head | |
| Stowers Proteomics | |
| contact affiliation | Stowers Institute for Med Res |
| contact email | proteomicslab@stowers.org |
| 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/MSV000102752/ |
