PXD039686

PXD039686 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Robust and easy-to-use one pot workflow for label free single cell proteomics
Description	The analysis of ultra-low input samples or even individual cells is essential to answering a multitude of biomedical questions, but current proteomic workflows are limited in their sensitivity and reproducibility. Here we report a comprehensive workflow that includes optimized strategies for all steps from cell lysis to data analysis. Thanks to convenient to handle 1 uL sample volume and standardized 384 well plates the workflow is easy for even novice users to implement. At the same time, it can be performed semi-automatized using the CellenONE, which allows for highest reproducibility. To achieve high throughput, ultrashort gradient lengths down to 5 min were tested using advanced u-pillar columns. Data-dependent acquisition (DDA), wide-window acquisition (WWA) and data-independent acquisition (DIA), and commonly used advanced data-analysis algorithms were bench-marked. Using DDA, 1790 proteins covering a dynamic range of four orders of magnitude were identified in a single cell. Using DIA, proteome coverage increased to more than 2200 proteins identified from single cell level input in a 20-min active gradient. The workflow enabled differentiation of two cell lines, demonstrating its suitability to cellular heterogeneity determination.
HostingRepository	MassIVE
AnnounceDate	2023-01-26
AnnouncementXML	Submission_2023-01-26_05:04:41.328.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Matzinger
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Oxidation
Instrument	Orbitrap Exploris 480

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-26 03:38:48	ID requested
⏵ 1	2023-01-26 05:04:41	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Single Cell Proteomics, one-pot workflow, label-free, WWA, DIA, uPAC, CellenONE

submitter keyword: Single Cell Proteomics, one-pot workflow, label-free, WWA, DIA, uPAC, CellenONE

Contact List

Manuel Matzinger
contact affiliation	IMP
contact email	manuel.matzinger@imp.ac.at
lab head
Karl Mechtler
contact affiliation	IMP, IMBA
contact email	mechtler@imp.ac.at
lab head
Manuel Matzinger
contact affiliation	IMP
contact email	manuel.matzinger@imp.ac.at
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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://massive.ucsd.edu/MSV000091156/

MassIVE dataset URI

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://massive.ucsd.edu/MSV000091156/