). We list a few we consider to be of particular use in core laboratories and will note which software does and which does not work within strict security and data privacy limitations. This table is by no means exhaustive and is complemented by an online database we make available on . To begin with, some software tools depend on a certain spike-in or QC material. For instance, QuiC (Biognosys) is a stand-alone software made for data containing the iRT peptide spike and is able to track QC metrics longitudinally. Though from a commercial company, this software is free to use and generates many of the ID-free and ID-based metrics discussed above using DDA, DIA, or targeted (i.e., SRM/PRM) analyses. The triple knock-out (TKO) visualization tool (TVT) is a web-portal that takes Thermo raw files as input. Though originally developed for the TMT11plex yeast material, the current version (2.5) supports all commercially available TMT sets up to and including TMT Pro 18-plex. The TVT provides numerous ID-based metrics using the known knockout proteomes, while also providing ID-free metrics like peak widths and injection time, and the ability to compare metrics between runs.