MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis

Abstract

Recently, mass spectrometry (MS) has emerged as an important tool for high-throughput screening (HTS) providing a direct and label-free detection method, complementing traditional fluorescent and colorimetric methodologies. Among the various MS techniques used for HTS, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) provides many of the characteristics required for high-throughput analyses, such as low cost, speed, and automation. However, visualization and analysis of the large datasets generated by HTS MALDI-MS can pose significant challenges, especially for multiparametric experiments. The datasets can be generated fast, and the complexity of the experimental data (e.g., screening many different sorbent phases, the sorbent mass, and the load, wash, and elution conditions) makes manual data analysis difficult. To address these challenges, a comprehensive informatics tool called MALDIViz was developed. This tool is an R-Shiny-based web application, accessible independently of the operating system and without the need to install any program locally. It has been designed to facilitate easy analysis and visualization of MALDI-MS datasets, comparison of multiplex experiments, and export of the analysis results to high-quality images.

Challenging the heterogeneity of disease presentation in malignant melanoma—impact on patient treatment

“…Then, representative spectra and peak lists (considering only the top 200 m/z values from each spectrum) of selected areas of interest were generated. The MALDIViz application was used to perform a comprehensive statistical analysis of the various peak lists (Jagadeesan and Ekstrom 2017). Multiple peaks were exclusively observed in specific tissue areas, but a large proportion of the signals showed a more general distribution within the tissue, represented as a Venn diagram (Fig.…”

Matrix-assisted laser desorption ionization mass spectrometry profiling of plasma exosomes evaluates osteosarcoma metastasis

“…Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has attracted increasing interests in clinical diagnosis with its high throughput, low sample consumption, label-free and direct analysis ability, easy operation, and low cost per sample characterization ( Jagadeesan and Ekstrom, 2017 ; Rathore et al., 2008 ). It has been used to identify bacterial pathogens by mass fingerprinting for clinical usage ( Varadi et al., 2017 ; Yi et al., 2018 , 2019 ) and determine treatment benefit from epidermal growth factor receptor inhibitors in patients with non-small cell lung cancer as a laboratory-developed clinical test ( Butts, 2014 ).…”

Advances in MALDI Mass Spectrometry within Drug Discovery

“…For example, Jagadeesan and coauthors 21 have applied molecular imprint technology for the capture and detection of progastrin-releasing peptide. Jagadeesan and Ekström 22 have further developed a visualization tool for MALDI data that can be quickly applied to the analysis of large datasets. Other articles discuss the identification of inhibitors of salt-inducible kinases, 23 in situ MALDI for screening the receptor tyrosine kinase cMET, 24 and quantitative imaging of tryptophan and kynurenine metabolites in antitumor immune response.…”