TCUP 1.1

|name| overview; input blast8, output estimated taxonomic composition and detected antibiotic resistance proteins.

TCUP uses peptides generated by mass spectrometry proteomics to:

  • identify and estimate the taxonomic composition of a microbial sample.
  • detect expressed antibiotic resistance proteins.

TCUP does not require a priori information about the contents of a sample and is suitable for analysis of both pure cultures, mixed samples, and clinical samples.

Read Introduction and overview for more details on how it works. If you prefer to throw yourself head-first into TCUP without first knowing the details of how it works, check out Installation right away to get started!


Authors:Fredrik Boulund

This is the documentation for TCUP version 1.1.0, last updated Sep 06, 2022. The documentation is available online at

TCUP is published as open-source under the ISC license and you are welcome to look at, suggest improvements, or download and improve/contribute to the code at the project’s Bitbucket page.

Citing TCUP

If you find TCUP useful, please cite the following paper that describes the method:

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, doi:10.1074/mcp.M116.061721


If you want to contribute to the development of TCUP, please refer to the CONTRIBUTING document in the root of the Bitbucket repository.

Indices and tables