hdacTR_data: TPP-TR example dataset.
In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description Details References See Also

Example subset of a dataset obtained by TPP-TR experiments to investigate possible targets for HDAC inhibitor Panobinostat.

hdacTR_data is a list of data frames that contain measurements for HDACs as well as a random selection of 500 further proteins.

You can use this dataset to explore the TPP package functionalities without invoking the whole time consuming analysis on the whole dataset.

The original dataset is located in the folder 'example_data/TR_example_data' in the package's installation directory. You can find it on your system by the R command system.file('example_data', package = 'TPP').

The measurements were generated by four separate multiplexed TMT experiments with 10 TMT labels each. Quantitative values per protein were obtained by the python software isobarQuant and converted to fold changes relative to the lowest temperature. The raw data before quantification can be found in the proteomicsDB database (http://www.proteomicsdb.org/#projects/4221/3101) with the following sample mapping:

Panobinostat_1: MS-experiment numbers P85192B02-B10
Panobinostat_2: MS-experiment numbers P85881B02-B10
Vehicle_1: MS-experiment numbers P85202B02-B10
Vehicle_2: MS-experiment numbers P85891B02-B10

Franken, H, Mathieson, T, Childs, D. Sweetman, G. Werner, T. Huber, W. & Savitski, M. M. (2015), Thermal proteome profiling for unbiased identification of drug targets and detection of downstream effectors. Nature protocols 10(10), 1567-1593.

hdacTR_smallExample, hdacTR_config

DoroChilds/TPP documentation built on Oct. 31, 2021, 4:38 a.m.