Affiliation:
1. Department of Biochemistry Charité – Universitätsmedizin Berlin Berlin Germany
2. Core Facility High‐Throughput Mass Spectrometry Charité – Universitätsmedizin Berlin Berlin Germany
3. The Wellcome Centre for Human Genetics, Nuffield Department of Medicine University of Oxford Oxford UK
4. Max Planck Institute for Molecular Genetics Berlin Germany
Abstract
AbstractIncreased 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. For instance, when benchmarking our workflow using a 500‐μL/min flow rate and 3‐min chromatographic gradients, we report the quantification of 5211 proteins from 2 μg of a mammalian cell‐line standard at high quantitative accuracy and precision. We further used this platform to analyze blood plasma samples from a cohort of COVID‐19 inpatients, using a 3‐min chromatographic gradient and alternating column regeneration on a dual pump system. The method delivered a comprehensive view of the COVID‐19 plasma proteome, allowing classification of the patients according to disease severity and revealing plasma biomarker candidates.
Funder
European Research Council
Bundesministerium für Bildung und Forschung
Subject
Molecular Biology,Biochemistry
Cited by
3 articles.
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