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
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