Install required dependencies

To make sure all the required pachages are installed run the install.R file in the parent folder of the cloned repo.

Assuming that git repository has benn cloned in the home directory and the application folder location is /home/ubuntu/maxquant-quant-analysis-public then run:

app_folder = "/home/ubuntu/maxquant-quant-analysis-public/"
source(file = file.path(app_folder, "install.R"))

Set up enviroinment

Input folder setup

The first step is to assign variables that point to the location of the maxquant output files and to the cloned git repository.

mq_folder = "/home/ubuntu/data/mq-test/"
app_folder = "/home/peppe/maxquant-quant-analysis-public/"

The mq_folder has to contain these files:

  • evidence.txt
  • modificationSpecificPeptides.txt
  • msms.txt
  • parameters.txt
  • peptides.txt
  • proteinGroups.txt
  • summary.txt

Experimental design info

Experimental dessign needs to be written in a tab separated file formatted like the example below:

file_name replicate experiment mqExperiment
JD_06232014_sample1_A 1 sample1 1_A
JD_06232014_sample1_B 2 sample1 1_B
JD_06232014_sample1_C 3 sample1 1_C
JD_06232014_sample2_A 1 sample2 2_A
JD_06232014_sample2_B 2 sample2 2_B
JD_06232014_sample2_C 3 sample2 2_C
JD_06232014_sample3_A 1 sample3 3_A
JD_06232014_sample3_B 2 sample3 3_B
JD_06232014_sample3_C 3 sample3 3_C
JD_06232014_sample4_A 1 sample4 4_A
JD_06232014_sample4_B 2 sample4 4_B
JD_06232014_sample4_C 3 sample4 4_C

Where the column file_name contains the names of the LC-MS/MS runs in the data, the column experiment contains the experimental conditions, the column replicate is a unique number for each of the biological or technical replicate in one experimental contition, the column mqExperiment contains the values in the “Experiment” column in the Maxquant “Raw data” tab when setting up the Maxquant analysis (figure below).

Maxquant experimental set up. Each “File” has to be associated to a unique value in the “Experiment” column

Maxquant experimental set up. Each “File” has to be associated to a unique value in the “Experiment” column

Imputation parameters

Missing values imputation is done as described in the paper here

Imputation parameters can be changed by altering the default values in the mq_transfomer function:

run_analysis <- mq_transfomer(app_folder = app_folder, 
                              mq_folder = mq_folder, 
                              expdes_filename = experimentalDesign_filename,
                              imputeStDev = 0.3,
                              imputePosition = 1.8)