PXD027912-3

PXD027912 is an original dataset announced via ProteomeXchange.

Title	Quantitative accuracy and precision in multiplexed single-cell proteomics.
Description	Multiplexed 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:31:00.327.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;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-12 15:15:51	ID requested
1	2022-01-28 01:25:07	announced
2	2023-05-14 14:19:40	announced	2023-05-14: Updated project metadata.
⏵ 3	2024-10-22 05:31:01	announced	2024-10-22: Updated project metadata.

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]

ProteomeXchange project tag: EPIC-XS

submitter keyword: Single-cell proteomics, benchmarking

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. 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 email	karl.mechtler@imp.ac.at
lab head
Claudia Ctortecka
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/2022/01/PXD027912

PRIDE project URI

• PRIDE
  1. PXD027912
     1. Label: PRIDE project
     2. Name: Quantitative accuracy and precision in multiplexed single-cell proteomics.