PXD056409 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics |
| Description | We assessed two physical disruption methods to homogenize cells —sonication and BeatBox—alongside four digestion protocols. Two of them are lab-reagent strategies: urea-based, and SDC (Sodium deoxycholate)-based in-solution digestion, and two are commercially available kits: the EasyPep kit from Thermo Fisher Scientific and S-Trap from Protifi. Each method's efficacy was evaluated based on protein recovery, peptide yield, and number of unique proteins identified through LC-MS analysis. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-01-07 |
| AnnouncementXML | Submission_2026-01-07_10:20:17.752.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Travis Uslan |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
| Instrument | Q Exactive HF |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2024-09-30 17:12:23 | ID requested | |
| ⏵ 1 | 2026-01-07 10:20:18 | announced | |
Publication List
| 10.1021/acsomega.4c11585; |
| Uslan T, Quan B, Wang TY, Pang M, Qiu Y, Chou TF, In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics. ACS Omega, 10(10):10642-10652(2025) [pubmed] |
Keyword List
| submitter keyword: In-solution digestion, LC-MS,Proteomics, proteolysis, Bottom-up proteomics |
Contact List
| Tsui-fen Chou |
|---|
| contact affiliation | Division of Biology and Biological Engineering, Chou Lab, Caltech, United States |
| contact email | tfchou@caltech.edu |
| lab head | |
| Travis Uslan |
|---|
| contact affiliation | Caltech |
| contact email | travisuslan@hotmail.com |
| dataset submitter | |
Full Dataset Link List
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://ftp.pride.ebi.ac.uk/pride/data/archive/2026/01/PXD056409 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD056409
- Label: PRIDE project
- Name: In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics
