Analysis of TMT-MS3 proteomics data with MaxQuant
missed_cleavage_rate.py , tmt_labeling_efficiency.py and percent_cysteines.py are for use with the modificationSpecificPeptides.txt output file from MaxQuant from the sample quality control step
map_gene_symbol.py and k_means_clustering.py are for use with the proteinGroups.txt output file from MaxQuant
USAGE: Use of these scripts assumed you have installed and run MaxQuant on your desktop. If you have installed it elsewhere please modify the directory accordingly.
Download the script and place it in Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt
Open the terminal by simultaneously pressing windows button + R
type cmd and press enter
type cd Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt and press enter
type python tmt_labeling_efficiency.py and press enter
Download the script and place it in Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt
Open the terminal by simultaneously pressing windows button + R
type cmd and press enter
type cd Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt and press enter
type python missed_cleavage_rate.py --protease <protease_name> where <protease_name> is lysc or trypsin
eg: python missed_cleavage_rate.py --protease lysc
eg: python missed_cleavage_rate.py --protease trypsin
Download the script and place it in Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt
Open the terminal by simultaneously pressing windows button + R
type cmd and press enter
type cd Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt and press enter
type python percent_cysteines.py and press enter
Download PHROG_annotation.csv from the PHROG_annotation.zip file on https://scholar.princeton.edu/wuehr/sample_prep and place into the txt MaxQuant folder (eg. Desktop\MaxQuant_1.6.0.16\MaxQuant\24fracs\combined\txt)
Download map_gene_symbol.py and place it in Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt
Open the terminal by simultaneously pressing windows button + R
type cmd and press enter
type cd Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt and press enter
type python map_gene_symbol.py and press enter
Download the script and place it in the appropriate txt MaxQuant folder as above
This must be in the same folder as where map_gene_symbol.py was placed and executed
Open the terminal by simultaneously pressing windows button + R
type cmd and press enter
type (eg.) cd Desktop\MaxQuant_1.6.0.16\MaxQuant\combined\txt and press enter
type python k_means_clustering.py --num_clusters --line_opacity --folder_name where you replace with an integer such as 4 which will be the number of clusters used by the k means clustering algorithm replace with a float such as .01 to tune the opacity of the individual lines of the protein plots generated replace with the desired folder name you wish to create
eg. python k_means_clustering.py --num_clusters 4 --line_opacity .01 --folder_name clustering_results
This will output all results into the newly created folder clustering_results