Peptide and Protein quantification from ionbot result files with command line FlashLFQ.
Install FlashLFQ as a docker image:
docker pull smithchemwisc/flashlfq:1.0.3
usage: ionbot2FlashLFQ.py [-h] [-x] folder [folder ...]
ionbot.quant: conver ionbot result files to FlashLFQ input file
positional arguments:
folder folder with ionbot results
optional arguments:
-h, --help show this help message and exit
-x don't filter peptide matches with unexpected modification
Each sample in an experiment is searched by ionbot with all fractions of the same sample in one search (to allow for correct protein inference).
Let's say we have ionbot results for an experiment with 3 samples in folders /home/sample1, /home/sample2 and /home/sample3.
Then the following script parses the ionbot.first.csv and ionbot.first.proteins.csv result files for each sample in an experiment:
python ionbot2FlashLFQ.py /home/sample1 /home/sample2 /home/sample3
It filters for identified PSMs (q-value <= 0.01) not shared between protein groups (read from the ionbot.first.proteins.csv files) and writes a flashlfq.tsv result file suitable for quantification by FlashLFQ.
Peptide matches with an unexpected modification are not used for protein quantification. This can be overruled by setting the -x flag.
The File Name column in flashlfq.tsv points to the spectrum file (can be a fraction) in which the PSM was identified (FlashLFQ in linux reads .mzML files for matching M1 data).
Copy the flashlfq.tsv file to the folder that contains all corresponding .mzML files and run (in that folder):
docker run --rm -v `pwd`:/mnt/data smithchemwisc/flashlfq:1.0.3 --idt /mnt/data/flashlfq.tsv --rep /mnt/data --mbr
This will quantify al identified peptides and proteins with the Matching Between Runs option enabled.