Proteomics

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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): Homo Sapiens (human) Escherichia Coli

TISSUE(S): Blood Plasma

SUBMITTER: Lukasz Szyrwiel  

LAB HEAD: prof. Markus Ralser

PROVIDER: PXD040205 | Pride | 2023-07-03

REPOSITORIES: pride

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Dataset's files

Source:
Action DRS
Benchamrking_5min-series.zip Other
Benchmarking_3min-series.log.txt Txt
Benchmarking_3min-series.zip Other
Benchmarking_5min-series.log.txt Txt
Ecoli-K12-uniprot-proteome_UP000000625-canonical-220529.fasta Fasta
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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]

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