Batch Effects in MALDI Mass Spectrometry Imaging

Benjamin Balluff*, Carsten Hopf, Tiffany Porta Siegel, Heike Grabsch, Ron M. A. Heeren

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Web of Science)


Mass spectrometry imaging (MSI) has become an indispensible tool for spatially resolved molecular investigation of tissues. One of the key application areas is biomedical research, where matrix-assisted laser desorption/ionization (MALDI) MSI is predominantly used due to its high-throughput capability, flexibility in the molecular class to investigate, and ability to achieve single cell spatial resolution. While many of the initial technical challenges have now been resolved, so-called batch effects, a phenomenon already known from other omics fields, appear to significantly impede reliable comparison of data from particular midsized studies typically performed in translational clinical research. This critical insight will discuss at what levels (pixel, section, slide, time, and location) batch effects can manifest themselves in MALDI-MSI data and what consequences this might have for biomarker discovery or multivariate classification. Finally, measures are presented that could be taken to recognize and/or minimize these potentially detrimental effects, and an outlook is provided on what is still needed to ultimately overcome these effects.

Original languageEnglish
Pages (from-to)628-635
Number of pages8
JournalJournal of the American Society for Mass Spectrometry
Issue number3
Publication statusPublished - 3 Mar 2021



Cite this