⮝ Full datasets listing
PXD067958-1
PXD067958 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Definitive benchmarking of DDA and DIA for host cell protein analysis on the Orbitrap Astral in a regulatory-aligned framework |
| Description | Host cell proteins (HCPs) are critical quality attributes in biotherapeutics that require accurate, specific, and comprehensive quantification. Mass spectrometry (MS)-based workflows are increasingly adopted to overcome the coverage and specificity limitations of immunoassays. This study benchmarks the performance of the Orbitrap Astral mass spectrometer for label-free HCP analysis, comparing data-dependent acquisition (DDA, Top80) and data-independent acquisition (DIA, 4 m/z non-staggered windows) modes. We applied a statistically rigorous framework integrating a stable isotope-labeled HCP mixture for traceable quantification, entrapment-based empirical false discovery proportion estimation, deterministic protein inference, and stratified bootstrapping. Both acquisition modes demonstrated exceptional quantitative fidelity. DIA outperformed DDA in identifications, yielding 45% more proteins and 68% more peptides. Hierarchical Bayesian modeling revealed superior differential linearity in DIA (mean slope 1.0) compared to DDA (slope 0.8). Stratified bootstrap analysis confirmed linearity and accuracy across the dynamic range, with DIA achieving lower limits of quantification (0.6 ppm) versus DDA (1.6 ppm). While both workflows reliably quantified most high-risk HCPs, DIA provided expanded proteome coverage and enhanced fold-change precision. These findings validate the Orbitrap Astral as a high-fidelity platform for HCP analysis in both modes and establish a defensible, regulatory-aligned MS-based framework for routine use in quality control environments. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-11-09 |
| AnnouncementXML | Submission_2025-11-09_06:48:03.583.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Somar |
| SpeciesList | scientific name: Cricetulus griseus; common name: Chinese hamster; NCBI TaxID: 10029; |
| ModificationList | Carbamidomethyl; Oxidation; Acetyl; Label:13C(6)15N(2); Label:13C(6)15N(4) |
| Instrument | Orbitrap Astral |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-09-01 13:06:53 | ID requested | |
| ⏵ 1 | 2025-11-09 06:48:04 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: HCP, DDA, DIA, Orbitrap Astral, Host cell protein, DatasetType:Proteomics |
Contact List
| Somar Khalil | |
|---|---|
| contact affiliation | GSK |
| contact email | somar.x.khalil@gsk.com |
| lab head | |
| Somar | |
| contact affiliation | GSK |
| contact email | somar.x.khalil@gsk.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/v10/MSV000098998/ |
