hdacCCR_data: TPP-CCR example dataset (replicates 1 and 2)
In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Example subset of a Panobinostat TPP-CCR dataset (replicates 1 and 2)

A list with two subsets of a dataset obtained by TPP-CCR experiments to investigate drug effects for HDAC inhibitor Panobinostat. It contains 7 HDACs as well as a random selection of 493 further proteins.

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

The original dataset is located in the folder 'example_data/CCR_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/4221/3102) with the following sample mapping:

Panobinostat_1: MS-experiment numbers P97404B02-B10
Panobinostat_2: MS-experiment numbers P97414B02-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.

hdacCCR_smallExample, hdacTR_config

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