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. Have a look in the online documentation to learn how to use TCUP.
- Authors
Fredrik Boulund
- Contact
- License
ISC
If you use TCUP in your work, please cite:
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.M116.061721To cite this repository, please use:
Detailed installation instructions are available in the online documentation.
Download and install Anaconda Python 3.5. Then create a conda environment and install TCUP into the environment using the following commands:
$ hg clone https://bitbucket.org/chalmersmathbioinformatics/tcup
$ conda env create -f ./tcup/conda_environment_Linux.yml
$ source activate tcup
$ pip install ./tcup/This will create a conda environment called tcup that contains all the required dependencies, and the tcup package itself.
TCUP depends on the following Python packages, easily installable via conda and pip.
- ETE Toolkit (ete3)
- XlsxWriter (xlsxwriter)
In order to run TCUP, some databases need to be prepared. Please consult the online documentation for details on how to build these.
The input for TCUP is mappings of peptides to reference genomes in blast8 tabular format. We recommend using BLAT or pBLAT for mapping.