PXD040455-2

PXD040455 is an original dataset announced via ProteomeXchange.

Title	HyperSCP: Combining Isotopic and Isobaric Labeling for Higher Throughput Single-Cell Proteomics
Description	Recent developments in mass spectrometry-based single-cell proteomics (SCP) have resulted in dramatically improved sensitivity, yet the relatively low measurement throughput remains a limitation. Isobaric and isotopic labeling methods have been separately applied to SCP to increase throughput through multiplexing. Here we combined both forms of labeling to achieve multiplicative scaling for higher throughput. Two-plex stable isotope labeling of amino acids in cell culture and isobaric Tandem Mass Tag labeling enabled up to 32 single cells to be analyzed in a single LC-MS analysis, in addition to reference and negative control channels. A custom nested nanowell chip was used for nanoliter sample processing to minimize sample losses. Using a 145-min total LC-MS cycle time, ~280 single cells were analyzed per day, which could be increased to ~700 samples per day with a high-duty-cycle multicolumn LC system producing the same active gradient. The labeling efficiency and achievable proteome coverage were characterized for multiple analysis conditions. Despite some decrease in coverage, this method readily differentiated four different cell types and thus proves suitable for, e.g., rapid cell typing.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:02:04.466.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	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-27 06:15:09	ID requested
1	2023-07-11 12:39:16	announced
⏵ 2	2023-11-14 09:02:08	announced	2023-11-14: Updated project metadata.

Liang Y, Truong T, Saxton AJ, Boekweg H, Payne SH, Van Ry PM, Kelly RT, HyperSCP: Combining Isotopic and Isobaric Labeling for Higher Throughput Single-Cell Proteomics. Anal Chem, 95(20):8020-8027(2023) [pubmed]

submitter keyword: multiplex, single-cell proteomics,high-throughput

Ryan T. Kelly
contact affiliation	Department of Chemistry and Biochemistry, Brigham Young University
contact email	ryan@chem.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/2023/07/PXD040455

PRIDE project URI

• PRIDE
  1. PXD040455
     1. Label: PRIDE project
     2. Name: HyperSCP: Combining Isotopic and Isobaric Labeling for Higher Throughput Single-Cell Proteomics