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A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation
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Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics.

Torsten Müller1,2, Mauro A Cremonini3, Georg Kliewer1,2

  • 1German Cancer Research Center (DKFZ), Heidelberg, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|September 4, 2023
PubMed
Summary

Automated sample preparation using autoSP3 enhances reproducibility for mass spectrometry (MS)-based proteomics. This streamlined workflow processes numerous clinical samples efficiently for improved disease diagnostics and therapy development.

Keywords:
AutoSP3AutomationClinical proteomicsHigh throughputLow inputMass spectrometryProteomicsSP3Sample preparation

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Clinical Proteomics

Background:

  • Mass spectrometry (MS)-based proteomics is crucial for molecular profiling of clinical specimens.
  • Preanalytical sample processing reproducibility is a major hurdle, especially for large or limited-sample cohorts.
  • Current methods require improvement for routine clinical applications.

Purpose of the Study:

  • To develop a streamlined, automated workflow for clinical sample preparation.
  • To enhance reproducibility and efficiency in proteomic analysis of clinical specimens.
  • To enable high-throughput processing of diverse sample types.

Main Methods:

  • Development of automated sonication and single-pot solid-phase-enhanced sample preparation (autoSP3).
  • Integration of tissue lysis, protein extraction, cleanup, and proteolysis into a single workflow.
  • Utilizing an automated liquid handling platform for concurrent processing of 96 samples.

Main Results:

  • AutoSP3 enables concurrent processing of 96 clinical samples of various types (tissue, liquid biopsies, cells).
  • The workflow integrates all sample preparation steps, from lysis to proteolysis.
  • Direct interfacing with LC-MS allows for proteome analysis with high sensitivity and reproducibility.

Conclusions:

  • Automated sample preparation using autoSP3 significantly improves reproducibility in MS-based proteomics.
  • The autoSP3 workflow offers a streamlined, high-throughput solution for clinical proteomic profiling.
  • This method accelerates disease classification, diagnostics, and therapy development through efficient sample processing.