Dataset Information

Robust and easy-to-use one pot workflow for label free single cell proteomics

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Karl Mechtler Manuel Matzinger

PROVIDER: MSV000091156 | MassIVE | Thu Jan 26 03:38:00 GMT 2023

SECONDARY ACCESSION(S): PXD039686

REPOSITORIES: MassIVE

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Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics.

Matzinger Manuel M Müller Elisabeth E Dürnberger Gerhard G Pichler Peter P Mechtler Karl K

Analytical chemistry 20230220 9

The analysis of ultralow 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 improved strategies for all steps, from cell lysis to data analysis. Thanks to convenient-to-handle 1 μL sample volume and standardized 384-well plates, the workflow is easy for even novice users to implement. At the same time, it c ...[more]

PMID: 36802514

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