Batch Effects in MALDI Mass Spectrometry Imaging

Abstract

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.

Reproducible Lipid Alterations in Patient-Derived Breast Cancer Xenograft FFPE Tissue Identified with MALDI MSI for Pre-Clinical and Clinical Application

“…This may be explained by day-to-day technical variations due to differences in the performance of the mass spectrometer and sample preparation devices as well as changes in laboratory environmental conditions (e.g., temperature and humidity) [ 23 ]. Recently, batch effects, potential systematic sources of technical variation, were identified in MSI analysis of a large sample size by multivariate analysis of pixel-to-pixel, section-to-section, and slide-to-slide variations, suggesting existing approaches to mitigate the batch effects such as improved study design, quality controls, new normalization methods, and robust experimental workflows [ 24 ]. The importance of technical replicates in order to obtain a quantifiable variance and reproducibility should be a must for the development of any analytical method [ 25 ].…”

Tissue sample preparations for preclinical research determined by molecular imaging mass spectrometry using matrix‐assisted laser desorption/ionization

“…The solution for tissue‐specific ion suppression problems can also be applied to the isotope‐labeled homolog of the target compound as the internal standard. The signal from this internal standard can be used to normalize the signal of the appropriate target signal [85]. Considering the above, verifying the developed method and checking its reproducibility in different laboratories is necessary.…”

“…Another characteristic variable only for MALDI-IMS can appear on a pixel, section, and slide level. All these batch effects can affect the final results and their interpretation because they can mask the differences in profiles of biological samples (false-negative effect) or introduce inexistent changes (false-positive effect) [85].…”

Quantifying the Matrix Metalloproteinase 2 (MMP2) Spatially in Tissues by Probe via MALDI Imaging Mass Spectrometry

“…Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has become a powerful means of detection technology, which achieved more and more attention by clinical researchers ( Barre et al, 2019 ; Balluff et al, 2021 ). Based on this method, even the spatial location of biomarkers in the organization can be provided by means of visualization ( Shariatgorji et al, 2019 ).…”