In MassDynamics/lfq_processing: Processes Proteomics Files for Quantification.

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"))

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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).

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Quantitative analysis

To load the main function into the enviroinment run:

source(file = file.path(app_folder, "app/mq_transformer.R"))

Set up a variable with the name of the experiment design file, the function assumes the files is located in the same folder of the Maxquant output

experimentalDesign_filename <- "experimentDesign.txt"

Running the quantitative analysis:

run_analysis <- mq_transfomer(app_folder = app_folder, 
                              mq_folder = mq_folder, 
                              expdes_filename = experimentalDesign_filename)

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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)

MassDynamics/lfq_processing documentation built on May 4, 2023, 11:20 p.m.