PXD041879

PXD041879 is an original dataset announced via ProteomeXchange.

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

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.

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]

submitter keyword: Sample Preparation, Single-Cell Proteomics,LC-MSMS

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

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

• PRIDE
  1. PXD041879
     1. Label: PRIDE project
     2. Name: Rapid, One-step Sample Processing for Label-Free Single-Cell Proteomics