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PXD039686-1

PXD039686 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRobust and easy-to-use one pot workflow for label free single cell proteomics
DescriptionThe 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.
HostingRepositoryMassIVE
AnnounceDate2023-01-26
AnnouncementXMLSubmission_2023-01-26_05:04:41.328.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterManuel Matzinger
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListCarbamidomethyl; Oxidation
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-01-26 03:38:48ID requested
12023-01-26 05:04:41announced
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 affiliationIMP
contact emailmanuel.matzinger@imp.ac.at
lab head
Karl Mechtler
contact affiliationIMP, IMBA
contact emailmechtler@imp.ac.at
lab head
Manuel Matzinger
contact affiliationIMP
contact emailmanuel.matzinger@imp.ac.at
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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