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The Edge Effect in High-Throughput Proteomics: A Cautionary Tale.

Colleen B Maxwell1,2, Jatinderpal K Sandhu1,2, Thong H Cao1,2

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Journal of the American Society for Mass Spectrometry
|May 8, 2023
PubMed
Summary
This summary is machine-generated.

Researchers identified an "edge effect" in multiwell plates impacting mass spectrometry quality control for clinical proteomics. Methods using heating techniques and surrogate standards can normalize this intraplate variation.

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Area of Science:

  • Clinical proteomics
  • Mass spectrometry-based research
  • Biomarker discovery

Background:

  • High-throughput mass spectrometry is crucial for clinical research, demanding robust quality control for reproducibility and accuracy.
  • Multiplexed targeted liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) assays in multiwell plates are increasingly used for large cohort studies.
  • Batch effects, or technical variations, are common in large-scale proteomics, potentially confounding results.

Purpose of the Study:

  • To identify and characterize an intraplate batch effect, termed the "edge effect," in clinical proteomics settings.
  • To present methods for assessing and ameliorating this edge effect to improve data quality.

Main Methods:

  • Investigated temperature gradients within multiwell plates during LC-MS/MS analysis.
  • Assessed heating techniques for multiwell plates.
  • Incorporated surrogate standards to normalize intraplate variation.

Main Results:

  • Identified an "edge effect" caused by temperature gradients in multiwell plates, a previously unreported phenomenon in clinical proteomics.
  • Demonstrated that proper assessment of heating techniques and the use of surrogate standards can mitigate this intraplate variation.

Conclusions:

  • The edge effect is a significant source of technical variation in clinical proteomics using multiwell plates.
  • Implementing optimized heating and normalization strategies with surrogate standards can enhance the reliability of mass spectrometry-based clinical research.