Scores for standardization of on-tissue digestion of formalin-fixed paraffin-embedded tissue in MALDI-MS imaging

Erich, Katrin; Sammour, Denis A.; Marx, Alexander; Hopf, Carsten

doi:10.1016/j.bbapap.2016.08.020

Cited by 25 publications

(29 citation statements)

References 55 publications

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“…1 ). For systematic method development guided by design of experiment principles, we used scores such as , which reflects both the scattering of hyperspectral data in PCA space as well as the efficiency of discrimination between different data sets 18 (see Suppl. Methods for more detail).…”

Section: Resultsmentioning

confidence: 99%

Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping

Weigt

Sammour

Ulrich

et al. 2018

Sci Rep

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Recent advances in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have enabled whole cell-MALDI mass spectrometry biotyping of drug-treated cultured cells for rapid monitoring of known abundant pharmacodynamic protein markers such as polyacetylated histones. In contrast, generic and automated analytical workflows for discovery of such pharmacodynamic markers, in particular lipid markers, and their use in cellular tests of drug-like compounds are still lacking. Here, we introduce such a workflow and demonstrate its utility for cellular drug-response monitoring of BCR-ABL tyrosine kinase inhibitors in K562 leukemia cells: First, low-molecular mass features indicating drug responses are computationally extracted from groups of MALDI-TOF mass spectra. Then, the lipids/metabolites corresponding to these features are identified by MALDI-Fourier transformation mass spectrometry. To demonstrate utility of the method, we identify the potassium adduct of phosphatidylcholine PC(36:1) as well as heme B, a marker for erythroid differentiation, as markers for a label-free MALDI MS-based test of cellular responses to BCR-ABL inhibitors. Taken together, these results suggest that MALDI-TOF mass spectrometry of lipids and other low molecular mass metabolites could support cell-based drug profiling.

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Section: Resultsmentioning

confidence: 99%

Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping

Weigt

Sammour

Ulrich

et al. 2018

Sci Rep

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“…First, the spatial resolution of peptide MALDI–MSI was inferior to traditional microscopy, with raster sizes for FFPE samples generally being between 50 and 100 µm . Second, sample preparation protocols for peptide MALDI‐MSI of FFPE tissues require many steps that can potentially introduce variability . Added complications include: the variation in preanalytics with regard to the instrumentation, solvents, and paraffin used, and timing of each stage; individual laboratories tending to optimize their MALDI–MSI sample preparation and measurement protocols according to available instrumentation and research interest, and that few research projects source tissue samples from different sites.…”

Section: Introductionmentioning

confidence: 99%

Site‐to‐Site Reproducibility and Spatial Resolution in MALDI–MSI of Peptides from Formalin‐Fixed Paraffin‐Embedded Samples

Longuespée

Casadonte³

et al. 2019

Proteomics Clinical Apps

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Purpose To facilitate the transition of MALDI–MS Imaging (MALDI–MSI) from basic science to clinical application, it is necessary to analyze formalin‐fixed paraffin‐embedded (FFPE) tissues. The aim is to improve in situ tryptic digestion for MALDI–MSI of FFPE samples and determine if similar results would be reproducible if obtained from different sites. Experimental Design FFPE tissues (mouse intestine, human ovarian teratoma, tissue microarray of tumor entities sampled from three different sites) are prepared for MALDI–MSI. Samples are coated with trypsin using an automated sprayer then incubated using deliquescence to maintain a stable humid environment. After digestion, samples are sprayed with CHCA using the same spraying device and analyzed with a rapifleX MALDI Tissuetyper at 50 µm spatial resolution. Data are analyzed using flexImaging, SCiLS, and R. Results Trypsin application and digestion are identified as sources of variation and loss of spatial resolution in the MALDI–MSI of FFPE samples. Using the described workflow, it is possible to discriminate discrete histological features in different tissues and enabled different sites to generate images of similar quality when assessed by spatial segmentation and PCA. Conclusions and Clinical Relevance Spatial resolution and site‐to‐site reproducibility can be maintained by adhering to a standardized MALDI–MSI workflow.

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“…2 b). For on-tissue digestion, such quality controls have already been proposed [ 24 ] but are still missing for the matrix application.…”

Section: Discussionmentioning

confidence: 99%

Round robin study of formalin-fixed paraffin-embedded tissues in mass spectrometry imaging

et al. 2018

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Mass spectrometry imaging (MSI) has provided many results with translational character, which still have to be proven robust in large patient cohorts and across different centers. Although formalin-fixed paraffin-embedded (FFPE) specimens are most common in clinical practice, no MSI multicenter study has been reported for FFPE samples. Here, we report the results of the first round robin MSI study on FFPE tissues with the goal to investigate the consequences of inter- and intracenter technical variation on masking biological effects. A total of four centers were involved with similar MSI instrumentation and sample preparation equipment. A FFPE multi-organ tissue microarray containing eight different types of tissue was analyzed on a peptide and metabolite level, which enabled investigating different molecular and biological differences. Statistical analyses revealed that peptide intercenter variation was significantly lower and metabolite intercenter variation was significantly higher than the respective intracenter variations. When looking at relative univariate effects of mass signals with statistical discriminatory power, the metabolite data was more reproducible across centers compared to the peptide data. With respect to absolute effects (cross-center common intensity scale), multivariate classifiers were able to reach on average > 90% accuracy for peptides and > 80% for metabolites if trained with sufficient amount of cross-center data. Overall, our study showed that MSI data from FFPE samples could be reproduced to a high degree across centers. While metabolite data exhibited more reproducibility with respect to relative effects, peptide data-based classifiers were more directly transferable between centers and therefore more robust than expected. Graphical abstractᅟ Electronic supplementary materialThe online version of this article (10.1007/s00216-018-1216-2) contains supplementary material, which is available to authorized users.

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Scores for standardization of on-tissue digestion of formalin-fixed paraffin-embedded tissue in MALDI-MS imaging

Cited by 25 publications

References 55 publications

Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping

Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping

Site‐to‐Site Reproducibility and Spatial Resolution in MALDI–MSI of Peptides from Formalin‐Fixed Paraffin‐Embedded Samples

Round robin study of formalin-fixed paraffin-embedded tissues in mass spectrometry imaging

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