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Deisotoper + LADS

Developed by Arun Devabhaktuni and the Elias Lab at Stanford University.

SUPPORTED OS:

• Any linux platform with BASH and Python installed.

REQUIREMENTS:

• Python 2.6 or greater
• Python-dev(el) installed
• Sudo privileges may be necessary

PACKAGE INCLUDES:

• Bash script to install necessary third party libraries for LADS
• Bash script to run both deisotoper and LADS together
• Deisotoper with mzxml functionality
• LADS
• Libsvm source code
• Python NUMPY source code
• Python NetworkX source code
• Test data set with DTAs and test mzXML (only contains ms2 peaks)

TO CONFIGURE: To configure, enter the collowing command:

sh config.sh

with root access. This will unpack necessary files. If you do not have python installed, it will error out and tell you that it is needed to use our software.

TO RUN: To run, enter the following command:

sh wrap.sh -d INPUT -o OUTPUT -l MS_LEVEL (optional) -r RESTRICTIONS (optional)

where -d is the input mzXML file, -o is the desired return directory for LADS and LADS scoring, -l related so the MS level that deisotoper will search for, and -r is the single piece that you wish to run (optional). Input must be entered with full path. By default, if no output directory is given, this script will default to storing all DTAs and LADS output files to the input directory. If the MS level is not specified, then it will default to MS2. Writing to this directory will require write permissions, and in case you encounter a warning saying that no such directory existed, please run under eleveated access.

Possible MS levels: 1 = MS1 2 = MS2 3 = MS1 + MS2 4 = MS3 5 = MS1 + MS3 6 = MS2 + MS3 7 = MS1 + MS2 + MS3

Possible restrictions with -r:
deisotope = Only run deisotoper
lads = Only run LADS search
score = Only run LADS scoring function

FOR HELP: Enter:

sh wrap.sh -h

TO MODIFY RUNS: Change the wrap.sh file to modify the parameters that you wish to use on either deisotoper or LADS. To view the help menus, type "sh wrap.sh HELP". Modifying parameters will need to be done within the wrap.sh script for each individual program.

NOTE: Current scripts are set up with relative paths which are based on the current extracted organization. Moving files to different directories will cause scripts to break.

Sample data has been packaged with the executables to help in verification that all programs function properly. For the deisotoper, there is a test mzXML file that unpacks to ~13,000 dta files. For LADS, a test set of dtas at ~620. For LADS scoring, a test run through the test dtas provided.

TO RUN DEISOTOPER INDEPENDENTLY: Run the following command within the deisotoper directory:

php deisotoper_mzxml_conversion.php -n -f $INPUT -o $TMP -l $LEVEL

where -f represents the input mzXML file, -o represents the output directory where the returned dta files will be returned, and -l represents the desired scan levels that will be extracted.

TO RUN LADS INDEPENDENTLY: Run the following command:

sh wrap.sh -d INPUT -o OUTPUT -l MS_LEVEL (optional) -r RESTRICTIONS (optional)

where -d is the input directory for all DTA files to be used in the search, -o is the output directory where output.txt will be stored, and -r is is "lads". NOTE: only the input, output, and output for tee should be changed as all other parameters are used for various portions of LADS. Removal of these arguments will cause the program to crash.

TO RUN LADS SCORING INDIVIDUALLY: Run the following command:

sh wrap.sh -d INPUT -o OUTPUT -l MS_LEVEL (optional) -r RESTRICTIONS (optional)

where -d is the directory in which the LADS search output is, -o is the desired directory for scoring output, and -r is "score".

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