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Fast proteomics with dia-PASEF and analytical flow-rate chromatography

ABSTRACT: The presented approach is a combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and raw data processing using the DIA-NN software suite, to conduct fast, low-cost proteomic experiments that only require moderate sample amounts. The present dataset contains a series of benchmarks. Specifically, a dilution series of a K562 digest standard acquired using 5-minute and 3-minute chromatographic gradients, as well as a mixed-species human–E.coli benchmark for quantitative performance. We further demonstrate the application of the proposed approach to the analysis of plasma proteomes of COVID-19 patients, using a 3-minute gradient acquisition on a dual-column liquid chromatography system at a throughput of 398 samples/day.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: prof. Markus Ralser

PROVIDER: MSV000096202 | MassIVE | Thu Oct 24 14:57:00 BST 2024

SECONDARY ACCESSION(S): PXD040205

REPOSITORIES: MassIVE

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Fast proteomics with dia-PASEF and analytical flow-rate chromatography.

Szyrwiel Lukasz L Gille Christoph C Mülleder Michael M Demichev Vadim V Ralser Markus M

Proteomics 20230607 1-2

Increased throughput in proteomic experiments can improve accessibility of proteomic platforms, reduce costs, and facilitate new approaches in systems biology and biomedical research. Here we propose combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and data analysis with the DIA-NN software suite, to achieve high-quality proteomic experiments from limited sample amounts, at a throughput of up to 400 samples per day. Fo ...[more]

PMID: 37287406

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Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition

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