mass spectrometry images in imzML format: Biomap (Novartis, free), Datacube Explorer (AMOLF, free), EasyMSI (CEA), Mirion (JLU), MSiReader (NCSU, free) and SpectralAnalysis. For processing .imzML files with the free statistical and graphics language R, a collection of R scripts is available, which permits parallel-processing of large files on a local computer, a remote cluster or on the Amazon cloud. Another free statistical package for processing imzML and Analyze 7.5 data in R exists, Cardinal. SPUTNIK is an R package containing various filters to remove peaks characterized by an uncorrelated spatial distribution with the sample location or spatial randomness. Applications A remarkable ability of MSI is to find out the localization of biomolecules in tissues, even though there are no previous information about them. This feature has made MSI a unique tool for clinical research and pharmacological research. It provides information about biomolecular changes related with diseases by tracking proteins, lipids, and cell metabolism. For example, identifying biomakers by MSI can show detailed cancer diagnosis. In addition, low cost imaging for pharmaceuticals studies can be acquired, such as images of molecular signatures that would be indicative of treatment response for a specific drug or the effectiveness of a particular drug delivery method. Ion colocalization has been studied as a way to infer local interactions between biomolecules. Similarly to colocalization in microscopy imaging, correlation has been used to quantify the similarity between ion images and generate network models. Advantages, challenges and limitations The main advantage of MSI for studying the molecules location and distribution within the tissue is that this analysis can provide either greater selectivity, more information or more accuracy than others. Moreover, this tool requires less investment of time and resources for similar results. The table below shows a comparison of advantages and disadvantages of some available techniques, including MSI, correlated with drug distribution analysis. Notes Further reading "Imaging Trace Metals in Biological Systems" pp 81-134 in "Metals, Microbes and Minerals: The Biogeochemical Side of Life" (2021) pp xiv + 341. Authors Yu, Jyao; Harankhedkar, Shefali; Nabatilan, Arielle; Fahrni, Christopher; Walter de Gruyter, Berlin. Editors Kroneck, Peter M.H. and Sosa Torres, Martha. DOI 10.1515/9783110589771-004 References Mass spectrometry