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PreprintCited by 81Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies

Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition

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Vowinckel, Jakob, Zelezniak, Aleksej, Kibler, Artur, Bruderer, Roland, Muelleder, Michael, Reiter, Lukas, Ralser, Markus·2016·Scientific Reports
DOI 10.1101/073478PMC PMC5847575

Preprint — published as 10.1038/s41598-018-22610-4

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Abstract

While quantitative proteomics is a key technology in biological research, the routine industry and diagnostics application is so far still limited by a moderate throughput, data consistency and robustness. In part, the restrictions emerge in the proteomics dependency on nanolitre/minute flow rate chromatography that enables a high sensitivity, but is difficult to handle on large sample series, and on the stochastic nature in data-dependent acquisition strategies. We here establish and benchmark a label-free, quantitative proteomics platform that uses microlitre/minute flow rate chromatography in combination with data-independent SWATH acquisition. Being able to largely compensate for the loss of sensitivity by exploiting the analytical capacities of microflow chromatography, we show that microLC-SWATH-MS is able to precisely quantify up to 4000 proteins in an hour or less, enables the consistent processing of sample series in high-throughput, and gains quantification precisions comparable to targeted proteomic assays. MicroLC-SWATH-MS can hence routinely process hundreds to thousands of samples to systematically create precise, label free quantitative proteomes.

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Authors
Vowinckel, J., Zelezniak, A., Kibler, A., Bruderer, R., Muelleder, M., Reiter, L., & Ralser, M.
Affiliations
  • University of Cambridge (GB)
  • The Francis Crick Institute (GB)
Corresponding author
Ralser, Markus
ORCID
Venue
Scientific Reports
Publisher
openRxiv
Published
2016-09-05
Volume
8
Issue
1
Pages
4346-4346
ISSN
2045-2322 (ISSN-L)
DOI
10.1101/073478
PMC
PMC5847575
OpenAlex
W2805896072
Cited by
81
References
59
Citations by year
2026: 3 · 2025: 12 · 2024: 5 · 2023: 11 · 2022: 14 · 2021: 12 · 2020: 10 · 2019: 9 · 2018: 3 · 2017: 2
FWCI
3.67
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
  • Chalmers Research (Chalmers University of Technology) (submittedVersion)
Funders
  • Wellcome Trust (200829, 093735, 093735/Z/10/Z, RG 200829/Z/16/Z, RG 093735/Z/10/Z, 260809, FC001134, 200829/Z/16/Z)
  • Francis Crick Institute (10134, FC001134)
  • Cancer Research UK (FC001134)
  • European Commission (609409, LTFCOFUND2013)
  • Science for Life Laboratory
  • Medical Research Council (FC001134)
  • Biotechnology and Biological Sciences Research Council (BB/N015215/1, 200829/Z/16/Z)
  • FP7 Ideas: European Research Council (260809)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
Keywords
quantitative proteomics, label-free quantification, data-independent acquisition, SWATH, retention time correction, batch effect correction, high-throughput proteomics, cost reduction, human proteome, yeast proteome
MeSH terms
Chromatography, Liquid, Cost-Benefit Analysis, Humans, Peptides, Saccharomyces cerevisiae, Software, K562 Cells, Proteome, Saccharomyces cerevisiae Proteins, Proteomics, Tandem Mass Spectrometry

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