SDRF to MSstats configuration file

As suggested in the guidelines to convert from SDRF to MaxQuant the user needs to install the sdrf-pipelines tool.

Installing sdrf-pipelines

Installing with pip:

pip install sdrf-pipelines

Installing with conda:

conda install sdrf-pipelines

and update with:

conda update sdrf-pipelines

or use the docker container:

docker pull quay.io/biocontainers/sdrf-pipelines:<tag>

Convert to MSstats annotation file: Usage

parse_sdrf convert-msstats -s PXD000288.sdrf.tsv -o msstats.csv 

MSstasts options

-s : SDRF file

-c : Create conditions from provided (e.g., factor) columns as used by MSstats

-o : annotation out file path

-swath : from openswathtomsstats output to msstats default false

-mq : from maxquant output to msstats default false