PXD025999 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Development of a mass spectrometric method for the analysis of periplasmic proteins from Gram-negative bacteria |
Description | Mass spectrometry-based proteomics has emerged as a powerful technique in the field of clinical diagnostics but requires a multistep process for sample preparation. The purpose of clinical mass spectrometry is to detect and quantify protein targets using well-established methods. Here, we found that the osmotic shock (OS) process allowed us to reduce the salt concentration and simultaneously enrich periplasmic proteins, specifically target proteins associated with antibiotic resistance in Gram-negative bacteria. Furthermore, we demonstrated that an optimized condition of the OS lysis allows the highest sensitivity in the MS analysis, and the OS lysate containing the proteins of interest (e.g., KPC-2) can be directly injected into multiple mass spectrometers without desalting process. Our study provides a detergent-free, straightforward method for periplasmic protein analysis using mass spectrometry. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_07:26:31.883.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Dong Huey Cheon |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF-X |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-05-13 03:30:29 | ID requested | |
1 | 2023-09-06 00:29:05 | announced | |
⏵ 2 | 2023-11-14 07:26:32 | announced | 2023-11-14: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: osmotic shock lysis,Gram-negative bacteria, KPC-2 producing E. coli, bottom-up, top-down, OS supernatant, LC-MS/MS |
Contact List
Je-Hyun Baek |
contact affiliation | Research & Development Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul, Korea |
contact email | jhbaek@mf.seegene.com |
lab head | |
Dong Huey Cheon |
contact affiliation | Seegene Medical Foundation |
contact email | caam203@gmail.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/2023/09/PXD025999 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD025999
- Label: PRIDE project
- Name: Development of a mass spectrometric method for the analysis of periplasmic proteins from Gram-negative bacteria