PXD023574 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2021-05-17 |
AnnouncementXML | Submission_2021-12-02_07:15:44.001.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Claudia Ctortecka |
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: Ultra-low input samples, DIA-TMT, identification-independent |
Contact List
Karl Mechtler |
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 | |
Claudia Ctortecka |
contact affiliation | IMP |
contact email | claudia.ctortecka@imp.ac.at |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD023574
- Label: PRIDE project
- Name: Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition