5,000 proteins within an acceptable time frame and, surprisingly, that current software is unable to process such large data sets simultaneously. Beyond these analytical insights, this study provides protein expression information on 11,000 proteins in >1,200 tumor samples from six cancer entities representing the first comprehensive pan-cancer proteome resource for FFPE material to date. The authors believe that the current study provides useful guidance for planning large-scale FFPE proteome projects and is also of immediate utility to the scientific community as the data is publicly accessible via a custom-built ShinyApp enabling a wide range of analysis. This includes e. g. the quantitative comparison of proteins of interest between patients or cohorts or the discovery of protein fingerprints that represent the tissue of origin and proteins that are enriched in certain cancer entities.]]>