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

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.