PXD041879 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Rapid, One-step Sample Processing for Label-Free Single-Cell Proteomics |
Description | Sample preparation for single-cell proteomics is generally performed in a one-pot workflow with multiple dispensing and incubation steps. These hours-long workflows can be labor intensive and lead to long sample-to-answer times. Here we report a sample processing method that achieves cell lysis, protein denaturation and digestion in one hour with a single reagent dispensing step using commercially available high-temperature-stabilized proteases. Four different one-step reagent compositions were evaluated, and the mixture providing greatest proteome coverage was compared to the previously employed multi-step workflow. The one-step preparation increases proteome coverage relative to the multi-step workflow while minimizing labor input and the possibility of human error. We also compared sample recovery between previously used microfabricated glass nanowell chips and injection-molded polypropylene substrates, and found the polypropylene provided improved proteome coverage. Combined, the one-step sample preparation and the polypropylene substrates enabled identification of an average of nearly 2,400 proteins per cell using a standard data-dependent workflow with an Orbitrap mass spectrometer. As such, these advances significantly simplify sample preparation for single-cell proteomics and broaden accessibility with no compromise in terms of proteome coverage. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_09:05:47.085.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Ryan Kelly |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Eclipse; Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-04-28 10:33:24 | ID requested | |
1 | 2023-10-09 13:52:33 | announced | |
⏵ 2 | 2023-11-14 09:05:50 | announced | 2023-11-14: Updated project metadata. |
Publication List
Johnston SM, Webber KGI, Xie X, Truong T, Nydegger A, Lin HL, Nwosu A, Zhu Y, Kelly RT, Rapid, One-Step Sample Processing for Label-Free Single-Cell Proteomics. J Am Soc Mass Spectrom, 34(8):1701-1707(2023) [pubmed] |
Keyword List
submitter keyword: Sample Preparation, Single-Cell Proteomics,LC-MSMS |
Contact List
Dr Ryan T. Kelly |
contact affiliation | Department of Chemistry and Biochemistry, Brigham Young University |
contact email | ryan.kelly@byu.edu |
lab head | |
Ryan Kelly |
contact affiliation | Brigham Young University |
contact email | ryan.kelly@byu.edu |
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/2023/10/PXD041879 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD041879
- Label: PRIDE project
- Name: Rapid, One-step Sample Processing for Label-Free Single-Cell Proteomics