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Peer-reviewedCC BY 4.0STAR Protocols

Automated plate-to-peptide protocol for mass spectrometry sample preparation

  • Sibilla Sander1
  • Sophie Buchser1
  • Michael Stumpe1
  • Joern Dengjel1
  1. 1Department of Biology, University of Fribourg, Chemin Du Musée 10, 1700 Fribourg, Switzerland
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Abstract

Although advances in mass spectrometry now support proteomic screens of thousands of samples and sample preparation has been automated to match, most current protocols still start from pre-prepared cell lysates. Here, we present a protocol for automated mass spectrometry sample preparation starting at the cell culture plate level. We describe steps for cell seeding in 96-well plates, in-plate cell lysis, and single-pot solid-phase-enhanced sample preparation. This streamlined approach significantly reduces manual handling while yielding highly reproducible measurements from low cell numbers.

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Cite

BibTeXRIS
BibTeX
@article{sander2026automated,
  title = {{Automated plate-to-peptide protocol for mass spectrometry sample preparation}},
  author = {Sibilla Sander and Sophie Buchser and Michael Stumpe and Joern Dengjel},
  journal = {STAR Protocols},
  year = {2026},
  month = oct,
  doi = {10.1016/j.xpro.2026.104917},
  url = {https://doi.org/10.1016/j.xpro.2026.104917},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Automated plate-to-peptide protocol for mass spectrometry sample preparation
AU  - Sibilla Sander
AU  - Sophie Buchser
AU  - Michael Stumpe
AU  - Joern Dengjel
PY  - 2026
DA  - 2026/10/28
JO  - STAR Protocols
DO  - 10.1016/j.xpro.2026.104917
UR  - https://doi.org/10.1016/j.xpro.2026.104917
AB  - Although advances in mass spectrometry now support proteomic screens of thousands of samples and sample preparation has been automated to match, most current protocols still start from pre-prepared cell lysates. Here, we present a protocol for automated mass spectrometry sample preparation starting at the cell culture plate level. We describe steps for cell seeding in 96-well plates, in-plate cell lysis, and single-pot solid-phase-enhanced sample preparation. This streamlined approach significantly reduces manual handling while yielding highly reproducible measurements from low cell numbers.
SN  - 2666-1667
ER  -