PXD043355

PXD043355 is an original dataset announced via ProteomeXchange.

Title	Easy and Accessible Workflow for Label-Free Single-Cell Proteomics
Description	Single cell proteomics (SCP) can provide information that is unattainable through either bulk-scale protein measurements or single-cell profiling of other omes. Maximizing proteome coverage often requires custom instrumentation, consumables and reagents for sample processing and separations, which limits accessibility of SCP to a small number of specialized laboratories. Commercial platforms have become available for SCP cell isolation and sample preparation, but the high cost of these platforms and the technical expertise required for their operation place them out of reach of many interested laboratories. Here, we assessed the new HP D100 Single Cell Dispenser for label-free SCP. The low-cost instrument proved highly accurate and reproducible for dispensing reagents in the 200 nL to 2 µL range. We used the HP D100 to isolate and prepare single cells for SCP within 384-well PCR plates. When the well plates were immediately centrifuged following cell dispensing and again after reagent dispensing, we found that ~97% of wells that were identified in the instrument software as containing a single cell indeed provided proteome coverage expected of a single cell. The D100 Single Cell Dispenser combined with one-step sample processing provides a very rapid easy-to-use workflow for SCP with no reduction in proteome coverage relative to a nanowell-based workflow. The commercial well plates also facilitate autosampling with commercial instrumentation. Single cell samples were analyzed using home-packed 30-µm-i.d. nanoLC columns as well as commercially available 50-µm-i.d. columns. The commercial columns led to identification of ~35% fewer identified proteins. However, combined with the well plate-based preparation platform the presented workflow provides fully commercial and relatively low cost alternative for SCP sample preparations and separations, which should greatly broaden accessibility of SCP to other laboratories.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:05:58.742.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 Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-27 19:17:12	ID requested
1	2023-10-09 14:47:56	announced
⏵ 2	2023-11-14 09:06:00	announced	2023-11-14: Updated project metadata.

Sanchez-Avila X, Truong T, Xie X, Webber KGI, Johnston SM, Lin HL, Axtell NB, Puig-Sanvicens V, Kelly RT, Easy and Accessible Workflow for Label-Free Single-Cell Proteomics. J Am Soc Mass Spectrom, 34(10):2374-2380(2023) [pubmed]

submitter keyword: Exploris 480, HP D100 Single Cell Dispenser,Single-Cell proteomics

Ryan T. Kelly
contact affiliation	Department of Chemistry and Biochemistry, Brigham Young University (lab head)
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/PXD043355

PRIDE project URI

• PRIDE
  1. PXD043355
     1. Label: PRIDE project
     2. Name: Easy and Accessible Workflow for Label-Free Single-Cell Proteomics