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 |
Keyword List
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/ |