converters

A repository of scripts that convert MaxQuant output tables to simplify downstream analysis.

SDRF processing

Two scripts - one written in Python, another in R - with the same funtionality: receive the SDRF file, peptides.txt and proteinGroups.txt and create expression matrices and sample annotation table. Each of them takes 5 arguments (position-dependent):

1. Path to SDRF file
2. Path to peptides.txt file
3. Path to proteinGroups.txt file
4. Output folder path
5. 'Protein IDs' or 'Gene names' to choose a column to keep in the proteinGroups expression matrix (can also select by inputing 1 or 2 respectively)

Usage:

python ./create_tables.py <path/to/sdrf.tsv> <path/to/peptides.txt> <path/to/proteinGroups.txt> <path/to/output/folder> 1
Rscript ./create_tables.R <path/to/sdrf.tsv> <path/to/peptides.txt> <path/to/proteinGroups.txt> <path/to/output/folder> 1

By default the script will keep in sample annotation table only those columns from the SDRF file that don't have the same value in each row. This behaviour is controled by SKIP_REDUNDANT_COLUMNS constant.

Additional resourses:

Learn more about how to create SDRF files in MaxQuant and how to use them in Perseus for output annotation in the manual or our video tutorial.