Fragmentation Diagrams

This project helps creating fragmentation diagrams of mass spectrometer data collected with an XCalibur ready device.

Getting Started - plotting the first diagram

I - convert XCalibur .raw into readable .mzXML:

On a windows machine open cmd.exe in the folder where ReAdw.exe and zlib1.dll are installed (hold Strg-Tab and right click on folder - open folder with cmd.exe). Type in the following command (replace capital letters with your settings):

ReAdw --mzXML RawFiles\DDMMYYYY\PLANTNAME\FILENAME.raw

Of course the corresponding .raw ought to be in that folder first. After successful conversion you will have a FILENAME.mzXML file in this folder. It is important to keep this structure of folders for the next steps. So - we are ready for the next step.

II - select parts of file to extract:

In OS where the emzed2 environment is installed (e.g. Ubuntu 14.04) open a terminal and type:

source ~/emzed2/bin/activate

then

emzed.workbench

Open peak_extraction.py and edit the following variables:

• date = 'DDMMYYYY' - corresponding to date of measurement which is also set in RawFiles and previous step
• plant = 'PLANTNAME' - in accordance with folder structure of .mzXML file (like date variable!!)
• filename = 'FILENAME' - without .mzXML extension
• compound_to_analyse = 'MASSFragmentationmode' - e.g. '777PQD' or '645CID'
• version = 'VERSION' - e.g. 'Version1' - making multiple versions of one compound is recommended (e.g. isomer detection)
• beginID = SCAN - where isolation/measurement started - derive from XCalibur programm
• endID = SCAN - where isolation/measurement ended

Run programm with F5 or similar. Maybe repeat for different versions.

III - plotting and analysing (where the fun begins):

In OS where python 3.x environment is installed open folder where fragmentationDiagrams.py is located. Run the following:

python3.5 fragmentationDiagrams.py

A list of options opens - the rest should be self-explanatory. Just experiment a bit. Also with the peak tables generated and stored into a .csv file (bear in mind that everything you create is stored but can easily be overwritten by plotting again!)

Note on good practice: 

This repo contains all necessary programs - keep them in this folder and simply add/create folders RawFiles/DATEOFMEASUREMENT/PLANTNAME . Only ReAdW.exe needs to be run on a Windows machine. The rest works on e.g. Ubuntu 14.04 fine. If you want to use different file structures you are encouraged to change a bit of the code. It is just optimized for specific analyis so far!

Prerequisites

plotting and analysis of diagrams

File: fragmentationDiagrams.py

The plotting code should run in any python 3.x environment with standard scientific libraries installed:

• matplotlib - for plotting editable diagrams
• scipy
• numpy
• pandas - data manipulation
• sklearn - for filtering data with savitzky-golay filter

However in the developing process some errors occured with specific versions of the tools used. All the testing and development took place in a python 3.5.4 environment using matplotlib 2.1.0.

extracting of peaks and preparation for plotting

The code for extracting the peaks out of the .mzXML files received from ReAdW.exe is run in an emzed2 environment using python 2.7.

Keeping updated

If you want to keep updated with this repo run the following:

Clone fork

git clone https://github.com/Progklui/MassSpectraFragmentationDiagrams.git

Add remote from this repo in your forked repo

cd into/forked_repo
git remote add upstream https://github.com/Progklui/MassSpectraFragmentationDiagrams.git
git fetch upstream

Updating

git pull upstream master

Done!

Built With

• Jupyter - part of the programming environment used
• emzed - other part of programming environment used
• IonSource - used for file conversion

License

This project is licensed under the MIT License - see the LICENSE.md file for details