PXD023574

PXD023574 is an original dataset announced via ProteomeXchange.

Title	Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition
Description	Single cell transcriptomics have revolutionized fundamental understanding of basic biology and disease. Since transcripts often do not correlate with protein expression, it is paramount to complement transcriptomics approaches with proteome analysis at single cell resolution. Despite continuous technological improvements in sensitivity, mass spectrometry-based single cell proteomics ultimately faces the challenge of reproducibly comparing the protein expression profiles of thousands of individual cells. Here, we combine two hitherto opposing analytical strategies, DIA and Tandem-Mass-Tag (TMT)-multiplexing, to generate highly reproducible, quantitative proteome signatures from ultra-low input samples. While conventional, data-dependent shotgun proteomics (DDA) of ultra-low input samples critically suffers from the accumulation of missing values with increasing sample-cohort size, data-independent acquisition (DIA) strategies do usually not to take full advantage of isotope-encoded sample multiplexing. We also developed a novel, identification-independent proteomics data analysis pipeline to quantitatively compare DIA-TMT proteome signatures across hundreds of samples independent of their biological origin to identify cell types and single protein knockouts. We validate our approach using integrative data analysis of different human cell lines and standard database searches for knockouts of defined proteins. These data establish a novel and reproducible approach to markedly expand the numbers of proteins one detects from ultra-low input samples, such as single cells.
HostingRepository	PRIDE
AnnounceDate	2023-05-14
AnnouncementXML	Submission_2023-05-14_14:19:54.575.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	ClaudiaCtortecka
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-13 10:35:45	ID requested
1	2021-05-16 23:01:27	announced
2	2021-12-02 07:15:44	announced	2021-12-02: Updated publication reference for PubMed record(s): 34793982.
⏵ 3	2023-05-14 14:19:55	announced	2023-05-14: Updated project metadata.

Ctortecka C, Kr, š, š, á, kov, á G, Stejskal K, Penninger JM, Mendjan S, Mechtler K, Stadlmann J, Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition. Mol Cell Proteomics, 21(1):100177(2022) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: DIA-TMT, identification-independent,Ultra-low input samples

KarlMechtler
contact affiliation	Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria. Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
contact email	karl.mechtler@imp.ac.at
lab head
ClaudiaCtortecka
contact affiliation	IMP
contact email	claudia.ctortecka@imp.ac.at
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/2021/05/PXD023574

PRIDE project URI

• PRIDE
  1. PXD023574
     1. Label: PRIDE project
     2. Name: Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition