The main publication that describes TCUP is:

Fredrik Boulund, Roger Karlsson, Lucia Gonzales-Siles, Anna Johnning, Nahid Karami, Omar AL-Bayati, Christina Ahren, Edward R. B. Moore, and Erik Kristiansson
TCUP: Typing and characterization of bacteria using bottom-up tandem mass spectrometry proteomics
Mol Cell Proteomics mcp.M116.061721. First Published on April 18, 2017,
Keywords: mass spectrometry, proteomics, microbial identification, pathogenic bacteria, antibiotic resistance detection, LC-MS/MS

Other related publications:

Roger Karlsson, Lucia Gonzales-Siles, Fredrik Boulund, Liselott Svensson-Stadler, Susann Skovbjerg, Anders Karlsson, Max Davidson, Stefan Hulth, Erik Kristiansson, Edward R.B. Moore
Proteotyping: Proteomic characterization, classification and identification of microorganisms – A prospectus
Systematic and Applied Microbiology, Volume 38, Issue 4, June 2015, Pages 246-257, ISSN 0723-2020
Keywords: Proteotypingf Proteomics, Mass spectrometry, Microbial systematics