Program for processing ion mobility mass spectrometry (MS) and native MS data.

Windows binaries are available from mscalculator.com. They were compiled in Windows 7 64 bit, Windows 8 64 bit has also been tested and works fine.

Spectrum deconvolution can be run on spectrum list text files using AtroposGui.exe:

• The copy spectrum list button in Mass Lynx works for this on the G1 and G2.
• For other instrumentation, please put a pair of coordinates per line as so:
  • mz I
    • mz is mass to charge ratio
    • I is intensity

To run ImProcessor.exe which converts Synapt G1 data into Amphitrite data files:

• You need to install cygwin (32 bit only), and make sure the cygwin bin directory (C:\cygwin\bin usually) is in your path.
• You need to put cdt.dll into the Amphitrite folder (alongside the ImProcessor.exe file)
  • This is distributed with Waters Driftscope v2.1, and currently will not work with versions of the file shipped with the Synapt G2 and newer.
  • If you are unsure about which version you have, the correct one is ~64 kb, where newer versions are larger (~74 kb)
  • The default file location is C:\Driftscope\lib\cdt.ll

Do not move the exe files out of the Amphitrite folder or they will stop working

We have not compiled binaries for OS X or Linux but the program can be easily be run from the command line. Waters only have the binary used for reading their datafiles in a Windows format, so processing Synapy G1 ion mobility files into an Amphitrite compatible format has to be done in Windows.

• Python 2.x
• NumPy
• SciPy
• Matplotlib
• wxPython

To install the dependencies in Ubuntu, run the following command in the terminal:

sudo apt-get install python-numpy python-scipy python-matplotlib python-wxtools

On OS X, download the latest Python 2.x release and install it, then run the following command:

pip install numpy scipy matplotlib wx

I wrote a blog post with instructions for this, you can view it here.

Then to run one of the programs navigate to the program directory e.g.:

cd Amphitrite/gui/AtroposGui/

And launch the python file ending in ‘Gui’ e.g.:

python AtroposGui.py

If you have any problems please let us know on the Google group: https://groups.google.com/forum/#!forum/amphitrite-im-ms

Let us know your email address if you would like to be updated with new versions and bug fixes.