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Modulating the protein content of complex proteomes using acetonitrile.

João Prates1, Gonçalo Martins1, Hugo López-Fernández2

  • 1BIOSCOPE Group, LAQV-REQUIMTE, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal.

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|March 5, 2018
PubMed
Summary
This summary is machine-generated.

Acetonitrile effectively modulates proteome dynamic range in complex samples. This cost-effective tool aids in differentiating healthy individuals from lymphoma and myeloma patients using serum proteomics.

Keywords:
AcetonitrileBiomarkerCancerDiseaseMethodSample treatmentSerum

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Area of Science:

  • Proteomics
  • Biochemistry
  • Analytical Chemistry

Background:

  • Complex biological samples present challenges in proteomic analysis due to wide dynamic range.
  • Current methods for proteome modulation may be costly or complex.
  • Developing accessible tools for sample preparation is crucial for advancing proteomics.

Purpose of the Study:

  • To investigate acetonitrile as a cost-effective agent for modulating the dynamic range of complex proteomes.
  • To determine optimal acetonitrile concentrations for effective protein fractionation and subsequent analysis.
  • To assess the utility of acetonitrile-based fractionation for differentiating disease states in serum samples.

Main Methods:

  • Serum samples from healthy individuals and patients with lymphoma and myeloma were treated with varying acetonitrile concentrations (15% to 65% v/v).
  • Proteins were separated into supernatant and pellet fractions based on acetonitrile concentration.
  • Protein profiles were analyzed using Principal Component Analysis (PCA) and Clustering to assess sample differentiation.

Main Results:

  • Acetonitrile concentration influenced the pelleting of proteins above 70 kDa.
  • Effective proteomic profiling using PCA or Clustering was achieved with supernatants from >45% acetonitrile or pellets from 35% and 45% acetonitrile.
  • Serum samples from healthy, lymphoma, and myeloma groups were successfully differentiated and classified using 55% acetonitrile.

Conclusions:

  • Acetonitrile serves as a versatile and cost-effective tool for modulating proteome dynamic range in complex samples.
  • Specific acetonitrile concentrations enable selective protein fractionation, facilitating downstream proteomic analysis.
  • This approach demonstrates significant potential for clinical proteomics, particularly in disease biomarker discovery and patient stratification.