⮝ Full datasets listing
PXD068974
PXD068974 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Pairing FAIMS and DIA for Cysteine Chemoproteomics |
| Description | Mass spectrometry-based cysteine chemoproteomics has enabled the proteome-wide discovery of thousands of functional and potentially therapeutically relevant sites. While this technology is increasingly utilized both in academic and industrial settings, modest sample throughput and variability in terms of ratios and coverage are areas that still warrant further methodological innovation. Data-independent acquisition (DIA) and high-field asymmetric waveform ion mobility spectrometry (FAIMS) are two increasingly utilized modes of acquisition that offer the potential benefits of decreased missing values and increased data reproducibility across replicate experiments. Here we pair FAIMS and DIA to enhance cysteine chemoproteomics. Using DIA by Neural Networks (DIA-NN) processing together with MSstats and Frag-Pipe-Analyst (FPA) statistical analysis, we demonstrate high cysteine coverage and low variance quantification for our DIA-FAIMS platform. We extend our methodology to three applications, cysteine-reactive small molecule screening, defining the subcellular nuclear cysteinome, and pinpointing translation arrest-induced cysteine reactivity analysis, which in aggregate identified a total of 27,346 cysteines, including 2,235 not previously reported in the CysDB database. Taken together, our methodology and associated comparison of data analysis tools adds to the growing toolbox for chemoproteomics and should broadly inform studies geared toward site-centric proteomic analysis. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-03-26 |
| AnnouncementXML | Submission_2026-03-26_10:45:21.025.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Lara Holoidovsky |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Carbamidomethyl |
| Instrument | Orbitrap Eclipse |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-09-29 16:50:59 | ID requested | |
| ⏵ 1 | 2026-03-26 10:45:21 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Chemoproteomics, Cysteine, Mass-spectrometry, DIA, FAIMS, FragPipe-Analyst, MSstats, cysDB, DatasetType:Proteomics |
Contact List
| Keriann Backus, Ph.D. | |
|---|---|
| contact affiliation | UCLA |
| contact email | kbackus@mednet.ucla.edu |
| lab head | |
| Lara Holoidovsky | |
| contact affiliation | UCLA |
| contact email | lara.holoidov@gmail.com |
| 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/v11/MSV000099323/ |
