• MAGMa+ allows MAGMa metabolite identification with dynamic parameter selection.
• Disclaimer: The installation of MAGMa/MAGMa+ was only tested on a linux machine.
• Prerequisites: A working version of Python2.7 is required
• Remark: The MAGMa version provided here was originally written by: Lars Ridder

• Make sure you have all MAGMa dependencies installed

• the most important dependency is RDKit (http://www.rdkit.org/) with INCHI support.

• other required python libaries are: sqlalchemy, lxml, numpy, pp, requests, macauthlib, mock, nose, coverage, sklearn

• Copy all the MAGMa/MAGMa+ source files and accompanying files to a dedicated directory.

• Setting up the shell environment: MAGMAPLUS_CLASSIFIER_PATH

  If the classifier files and AllFingerprints.txt file are in a different directory than the one you run MAGMa+ from, the MAGMAPLUS_CLASSIFIER_PATH variable should be set to that different directory. It should contain: AllFingerprints.txt, metabolite_posD_rfc.pkl and metabolite_negC_rfc.pkl

• Unzip the classifier pickle files (metabolite_posD_rfc.pkl.zip and metabolite_negC_rfc.pkl.zip).

• Creating a configuration file

  A magma_job.ini config file is read from working directory.

  Example content:

	[magma job]
	# Location of structure database to fetch candidate molecules to match against ms peak trees
	# db is expected to be available at where job is executed
	structure_database.hmdb = /path/to/HMDB_MAGMa.db
	chemical_engine = rdkit

• Generating a molecular structure database.

  A script (process_hmdb.py) is provided that generates an HMDB database. It can be adapted at will to generate other structure databases.

• Run MAGMa+ exactly as you would run MAGMa. For more information, type:

	python /path_to_magma_plus/MAGMa_plus.py -h

• Example:

	export MAGMAPLUS_CLASSIFIER_PATH=/path/to/classifiers
	echo '100.112725211: 100 (53.0388: 0.836306820171, 55.0544: 25.3576989727, 58.029: 0.108793463482, 83.0855: 100.0)' > example.tree
	python MAGMa_plus.py read_ms_data -i 1 -p 5 -q 0.001 -f mass_tree example.tree output.db
	python MAGMa_plus.py annotate -c 0 -d 0 -b 3 -w 1 -s hmdb output.db
	python MAGMa_plus.py export_result output.db

Please cite the papers:

• http://link.springer.com/article/10.1007%2Fs11306-016-1036-3
• http://onlinelibrary.wiley.com/doi/10.1002/rcm.6364/full