This repository contains some hopefully useful tools for mass spectrometry applied to proteomics. Speficically, it contains

• the TAPIR visualization software (available in ./gui)
• the MS Proteomics Tools Library (available in ./msproteomicstoolslib)
• a set of executables and scripts (available under ./analysis)

The code is under the 3-clause BSD licence (see the LICENSE and the AUTHORS files).

TAPIR is a software that allows visualization of targeted proteomics data. See the TAPIR install instructions for further information on installation.

Please also see the project homepage for further information. Binaries are available for Windows and Mac OS X. For a source installation of the package, see below.

The mass spectrometric (MS) Proteomics Tools Library contains multiple Python functions useful for MS-based proteomics.

Documentation for the library can be found at http://proteomics.ethz.ch/msproteomicstools/ which contains source code documentation of the available functions and objects.

After installing the dependencies, you can proceed to install msproteomicstools itself:

pip install numpy
pip install msproteomicstools

Alternatively, a source install can be chosen as well:

git checkout https://github.com/msproteomicstools/msproteomicstools.git
pip install numpy
python setup.py install --prefix=/your/install/path 

There are some extra packages that can increase the features and improve the speed of the toolset

To get fast lowess performance (several orders of magnitude faster), do the following

git clone https://github.com/carljv/Will_it_Python.git
cd Will_it_Python/MLFH/CH2/lowess\ work/
python setup.py build
sudo python setup.py install