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Updated: Jul 1, 2026

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation
07:12

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

Published on: April 24, 2020

A high confidence, manually validated human blood plasma protein reference set.

Susann Schenk1, Gary J Schoenhals, Gustavo de Souza

  • 1Department of Biochemistry and Molecular Biology, Bioinformatics, University of Southern Denmark, Campusvej 55, 5230 Odense M,Denmark. sschenk@bmb.sdu.dk

BMC Medical Genomics
|September 17, 2008
PubMed
Summary
This summary is machine-generated.

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Researchers identified 697 high-confidence human plasma proteins using advanced mass spectrometry. This ultra-high confidence protein list advances biomarker discovery and the diagnostic potential of blood plasma.

Area of Science:

  • Proteomics
  • Biomarker Discovery
  • Mass Spectrometry

Background:

  • Human plasma holds significant diagnostic potential, driving efforts to catalog its protein content.
  • Previous efforts, like the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP), faced challenges in establishing reliable protein lists.
  • A need exists for an ultra-high confidence (≥99%) reference list of plasma proteins to facilitate future biomarker discovery.

Purpose of the Study:

  • To establish an ultra-high confidence reference list of human plasma proteins.
  • To improve upon existing plasma protein datasets by employing more stringent validation criteria.
  • To facilitate future biomarker discovery and enhance the diagnostic utility of blood plasma.

Main Methods:

  • Utilized advanced mass spectrometry instruments: linear ion-trap-Fourier transform (LTQ-FT) and linear ion trap-Orbitrap (LTQ-Orbitrap).

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Using Reference Reagents to Confirm Robustness of Cytokine Release Assays for the Prediction of Monoclonal Antibody Safety
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Using Reference Reagents to Confirm Robustness of Cytokine Release Assays for the Prediction of Monoclonal Antibody Safety

Published on: September 15, 2023

Related Experiment Videos

Last Updated: Jul 1, 2026

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation
07:12

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

Published on: April 24, 2020

Using Reference Reagents to Confirm Robustness of Cytokine Release Assays for the Prediction of Monoclonal Antibody Safety
06:37

Using Reference Reagents to Confirm Robustness of Cytokine Release Assays for the Prediction of Monoclonal Antibody Safety

Published on: September 15, 2023

  • Employed MS3 (tandem mass spectrometry) with high mass accuracy (low ppm range) for confident peptide identification.
  • Applied rigorous statistical analysis and exclusion criteria (e.g., immunoglobulin family proteins) to ensure high confidence in the final protein list.

    • Main Results:

    • Established a high-confidence set of 697 blood plasma proteins.
    • Achieved high average sequence coverage (>14 peptides/protein, median 6 peptides/protein).
    • Compared results across different mass spectrometry instruments and separation techniques, validating the findings.

    Conclusions:

    • Superior instrumentation and rigorous validation yielded a 697-protein plasma list with very high confidence.
    • Demonstrated an exceptionally low false peptide identification rate of 0.29%.
    • This ultra-high confidence reference list is crucial for advancing plasma proteome research and biomarker discovery.