“…[6,29] The methods necessary to prepare FFPE samples, perform MALDI-IMS, analyze data and characterize the resulting peptide features have not yet been standardized and are largely developed in-house by individual laboratories. [6,7,14,30,31] As such, the need to add to the limited number of detailed protocols in the field [14] prompted the current manuscript, in which the methods developed and published in two previous manuscripts by our group [29,32] have been described in a single detailed experimental workflow combining tryptic peptide MALDI-IMS and subsequent liquid chromatographic/tandem mass spectrometric (LC/MS/MS) identification of the peptides which localize to a region of interest (e.g. tumour tissue).…”