Wrapper for running MSBlender for an experiment with multiple mxZMLs

Use the MSBlender branch consistent_search_params

git clone https://github.com/marcottelab/MSblender.git

git checkout consistent_search_params

On TACC or not TACC

Setup experiment directory

Start with a folder for each experiment containing a folder called mzXML containing its mzxml files and a folder called DB containing formatted fasta database. See below for how to make a formatted fasta

Structure of an experiment directory for experiment Ce1104

Ce1104_example

-----mzXML

---------- WAN1100427_OT2_Celegans_HCW_P1A01.mzXML

---------- WAN1100427_OT2_Celegans_HCW_P1A02.mzXML

-----DB

---------- uniprot-proteome%3AUP000001940_caeel_contam.combined.fasta

Write each experiment you want to process as one line in a list of experiment IDs

This can be a one line file with one experiment or multiline with multiple experiments

For example:

$ cat exp_list_example.txt
Ce1104_example

Create additional folders in the experiment directory

$ bash scripts/create_directory.sh $SCRATCH/metazoans/exp_list_example.txt

Format msblender commands for each mzXML in the experiments

Creates file for each experiment called [experimentID]_commands.txt

$ bash scripts/create_commands.sh exp_list_example.txt $WORK/MSblender/runMS2.sh $HOME/searchgui

Create the TACC job submission script to process the commands in parallel

Need to manually edit header in template_run_MS.sbatch

Creates file for each experiment called [experimentid]_run_MS.sbatch

$ bash scripts/create_sbatch.sh exp_list_example.txt

$ sbatch Ce_1104_example_run_MS.sbatch

If not on TACC, process the commands with parallel

$ parallel -j4 :::: Ce1104_COMMANDS.txt

Format fasta DB

This goes in /DB folder of each experiment

Can also format ahead of time for a proteome and just cp in to the DB folder

Add on contaminants and reverse proteome

$ bash $WORK/MSblender/setup/setup_database_only.sh uniprot-triticum%3AUP000019116.fasta

Generate blast formatted db

$ formatdb -i uniprot-triticum%3AUP000019116_contam.combined.fasta