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Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/MS

Nadine A Binai1, Fabio Marino, Peter Soendergaard

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Summary

This study introduces a rapid liquid chromatography (LC) system for faster proteomic analyses. The innovative setup significantly reduces analysis time, making it ideal for clinical proteomics applications with large sample volumes.

Keywords:
SPE−LCSTAGE tipsmass spectrometrynanoliquid chromatographyprotein analysisproteomes and interactomessolid-phase extraction

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Proteomics

Background:

  • Traditional proteomics workflows are time-consuming.
  • High-throughput analysis is crucial for clinical applications.
  • Optimizing liquid chromatography (LC) systems can improve efficiency.

Purpose of the Study:

  • To develop and evaluate a rapid LC system for enhanced proteomic analysis.
  • To assess the system's compatibility with various proteomics workflows.
  • To demonstrate the system's utility in clinical settings.

Main Methods:

  • Utilized disposable solid-phase extraction (SPE) cartridges and short LC-MS/MS gradients (<10 min).
  • Employed an autosampler with STAGE tips as precolumns and a short reversed-phase (RP) analytical column.
  • Integrated the system with offline prefractionation methods (1D gel electrophoresis, strong-cation exchange chromatography) and affinity purification interactome analysis.
  • Applied the system to shotgun proteomics experiments on AspN digested cell lysate.

Main Results:

  • Achieved proteomic analyses in under 10 minutes.
  • Successfully analyzed interactomes in approximately 1 hour.
  • Detected over 3600 protein groups in shotgun proteomics using 36 SCX fractions within 5.5 hours.
  • Maintained high proteomic detail despite reduced analysis time.

Conclusions:

  • The developed fast LC system significantly reduces proteome analysis time.
  • The system is versatile and integrates well with established proteomics workflows.
  • This rapid LC approach is highly relevant for clinical proteomics, enabling large-scale sample analysis with fast turnaround.