Here, we present a script to count the number of S,T,Y phosphorylated residues above a given threshold from MaxQuant data.
We provide an example input file Phospho(STY)Sites.txt to use our script with. To run the script on this data:
python3 phospho_maxquant_process.py ---maxQuantInFile Phospho(STY)Sites.txt
The output is written to by default to the file Output.txt (this can be changed using the option --outfile below).
The output file contains the S, T, Y counts in the last 6 columns. The first column shows the peptide identifier, and the second column shows the quantified phosphopeptide.
$ python3 phospho_maxquant_process.py -h
usage: phospho_maxquant_process.py [-h] --maxQuantInFile MAXQUANTINFILE
[--protColumn PROTCOLUMN]
[--locProbColumn LOCPROBCOLUMN]
[--locProbTh LOCPROBTH]
[--styProbColumn STYPROBCOLUMN]
[--styProbTh STYPROBTH] [--outfile OUTFILE]
Extract S, T and Y site counts (which are above thresholds) from MaxQuant
data.
optional arguments:
-h, --help show this help message and exit
--maxQuantInFile MAXQUANTINFILE
An output file from MaxQuant, as input to this script.
--protColumn PROTCOLUMN
Column containing the protein identifier. Default is
0.
--locProbColumn LOCPROBCOLUMN
Column containing the localization probability.
Default is 5.
--locProbTh LOCPROBTH
Threshold to filter localization probability (between
0 and 1). Default is 0.75.
--styProbColumn STYPROBCOLUMN
Column containing the phospho-(STY)-probabilities.
Default is 29.
--styProbTh STYPROBTH
Threshold to filter phospho-(STY)-probabilities
(between 0 and 1). Default is 0.75.
--outfile OUTFILE Output file to save the results to. Default is
Output.txt.