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Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics.

Ludwig R Sinn1, Lukasz Szyrwiel1, Justus Grossmann1

  • 1Department of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany.

Biorxiv : the Preprint Server for Biology
|September 15, 2025
PubMed
Summary
This summary is machine-generated.

Slice-PASEF enhances mass spectrometry (MS) sensitivity for quantitative proteomics. This new technology enables precise analysis of minimal sample amounts, advancing applications like single-cell proteomics and ubiquitinomics.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biotechnology

Background:

  • Quantitative mass spectrometry (MS)-based proteomics is a widely used technology.
  • Emerging applications like single-cell proteomics and spatial proteomics require high sensitivity for minimal sample amounts.
  • Current workflows are often limited by sensitivity when analyzing small samples.

Purpose of the Study:

  • To present Slice-PASEF, a novel mass spectrometry technology designed to maximize tandem MS sensitivity.
  • To demonstrate the capability of Slice-PASEF for precise quantitative proteomics with low sample inputs.
  • To showcase the utility of Slice-PASEF in advanced applications.

Main Methods:

  • Slice-PASEF utilizes trapped ion mobility separation of ions to achieve maximum theoretical tandem MS sensitivity.
  • A new module was developed in DIA-NN software to implement Slice-PASEF.
  • The technology was applied to various proteomic analyses, including single-cell proteomics and ubiquitinomics.

Main Results:

  • Slice-PASEF enables precise quantitative proteomics even with minimal sample amounts.
  • The technology significantly enhances the sensitivity of mass spectrometry workflows.
  • Demonstrated utility in single-cell proteomics and degrader drug screens via ubiquitinomics.

Conclusions:

  • Slice-PASEF represents a significant advancement in mass spectrometry sensitivity for proteomics.
  • This technology overcomes limitations in analyzing small sample quantities.
  • Slice-PASEF opens new possibilities for sensitive proteomic applications.