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Batch Effects in MALDI Mass Spectrometry Imaging.

Benjamin Balluff1, Carsten Hopf2, Tiffany Porta Siegel1

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Journal of the American Society for Mass Spectrometry
|February 1, 2021
PubMed
Summary
This summary is machine-generated.

Batch effects in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) hinder data comparison in biomedical research. This review details batch effect sources, impacts, and mitigation strategies for reliable MALDI-MSI analysis.

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Area of Science:

  • Biomedical research
  • Analytical chemistry
  • Data science

Background:

  • Mass spectrometry imaging (MSI) is crucial for spatial molecular analysis in tissues.
  • Matrix-assisted laser desorption/ionization (MALDI) MSI is widely used in biomedical research for its high throughput and flexibility.
  • Batch effects, common in omics, pose challenges for MALDI-MSI data comparability, especially in translational research.

Purpose of the Study:

  • To critically review batch effects in MALDI-MSI data.
  • To identify manifestation levels and consequences of batch effects.
  • To present strategies for recognizing, minimizing, and overcoming batch effects.

Main Methods:

  • Review of existing literature on batch effects in MALDI-MSI.
  • Analysis of batch effect origins at pixel, section, slide, time, and location levels.
  • Discussion of implications for biomarker discovery and classification.

Main Results:

  • Batch effects can arise at multiple levels in MALDI-MSI experiments.
  • These effects can significantly impact the reliability of biomarker discovery and multivariate classification.
  • Various strategies exist for mitigating batch effects, though complete elimination remains a challenge.

Conclusions:

  • Addressing batch effects is critical for robust MALDI-MSI data interpretation in translational research.
  • Further development is needed to fully overcome batch effects for reliable multi-study comparisons.
  • Implementing recognition and minimization strategies is essential for advancing the field.