PXD048179

PXD048179 is an original dataset announced via ProteomeXchange.

Title	Enhanced feature matching in single-cell proteomics characterizes response to IFN-γ and reveals co-existence of different cell states-single cell Proteomics experiment
Description	Proteome analysis by data-independent acquisition (DIA) has become a powerful approach to obtain deep proteome coverage, and has gained recent traction for label-free analysis of single cells. However, optimal experimental design for DIA-based single-cell proteomics has not been fully explored, and performance metrics of subsequent data analysis tools remain to be evaluated. Therefore, we here present DIA-ME, a data analysis strategy that exploits the co-analysis of low-input samples with a so-called matching enhancer (ME) of higher input, to increase sensitivity, proteome coverage, and data completeness. We evaluate the matching specificity of DIA-ME by a two-proteome model, and demonstrate that false discovery and false transfers are maintained at low levels when using DIA-NN software, while preserving quantification accuracy. We apply DIA-ME to investigate the proteome response of U-2 OS cells to interferon gamma (IFN-γ) in single cells, and recapitulate the time-resolved induction of IFN-γ response proteins as observed in bulk material. Moreover, we observe co- and anti-correlating patterns of protein expression within the same cell, indicating mutually exclusive protein modules and the co-existence of different cell states. Collectively our data show that DIA-ME is a powerful, scalable, and easy-to-implement strategy for single-cell proteomics.
HostingRepository	PRIDE
AnnounceDate	2024-08-22
AnnouncementXML	Submission_2024-08-22_12:43:02.218.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Syed Azmal Ali
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-30 03:21:35	ID requested
⏵ 1	2024-08-22 12:43:02	announced

Dataset with its publication pending

submitter keyword: Proteome analysis

Data-independent acquisition (DIA)

Single-cell proteomics

Label-free analysis

DIA-ME (Matching Enhancer)

DIA-NN software

Prof. Jeroen Krijgsveld
contact affiliation	1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany
contact email	j.krijgsveld@dkfz.de
lab head
Syed Azmal Ali
contact affiliation	German Cancer Research Center
contact email	azmal786@gmail.com
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/2024/08/PXD048179

PRIDE project URI

• PRIDE
  1. PXD048179
     1. Label: PRIDE project
     2. Name: Enhanced feature matching in single-cell proteomics characterizes response to IFN-γ and reveals co-existence of different cell states-single cell Proteomics experiment