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PXD027912

PXD027912 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleQuantitative accuracy and precision in multiplexed single-cell proteomics.
DescriptionMultiplexed quantitative mass spectrometry-based proteomics is shaped by numerous opposing propositions. With the emergence of multiplexed single-cell proteomics, studies increasingly present single cell measurements in conjunction with an abundant congruent carrier to improve precursor selection and enhance identifications. While these extreme carrier spikes are often >100-times more abundant than the investigated samples, undoubtedly the total ion current increases but quantitative accuracy possibly is affected. We here focus on narrowly titrated carrier spikes (i.e. <20x) and evaluate the elimination of such for comparable sensitivity at superior accuracy. We find that subtle changes in the carrier ratio can severely impact measurement variability and describe alternative multiplexing strategies to evaluate data quality. Lastly, we demonstrate elevated replicate overlap, while preserving acquisition throughput at improved quantitative accuracy with DIA-TMT and discuss optimized experimental designs for multiplexed proteomics of trace samples. This comprehensive benchmarking gives an overview of currently available techniques and guides through conceptualizing the optimal single-cell proteomics experiment.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:31:00.327.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterClaudia Ctortecka
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-08-12 15:15:51ID requested
12022-01-28 01:25:07announced
22023-05-14 14:19:40announced2023-05-14: Updated project metadata.
32024-10-22 05:31:01announced2024-10-22: Updated project metadata.
Publication List
10.1021/acs.analchem.1c04174;
Ctortecka C, Stejskal K, Kr, š, š, á, kov, á G, Mendjan S, Mechtler K, Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics. Anal Chem, 94(5):2434-2443(2022) [pubmed]
Keyword List
ProteomeXchange project tag: EPIC-XS
submitter keyword: Single-cell proteomics, benchmarking
Contact List
Karl Mechtler
contact affiliationResearch 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. The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
contact emailkarl.mechtler@imp.ac.at
lab head
Claudia Ctortecka
contact affiliationIMP
contact emailclaudia.ctortecka@imp.ac.at
dataset submitter
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Dataset FTP location
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