Some hopefully useful tools for mass spectrometry applied to proteomics
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Revert "[FIX] Acetylation / Carbamylation fix for TPP annotation"
Latest commit eeed765 Jun 18, 2018

README.md

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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) including the TRIC alignment tool

The code is under the 3-clause BSD licence (see the LICENSE and the AUTHORS files). For full documentation, see the online documentation.

Install

You can install the library and tools as follows:

pip install numpy
pip install pymzml==0.7.8
pip install Biopython
pip install msproteomicstools

Fast lowess

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

TRIC

The ./analysis folder contains the TRIC alignment tool, see the TRIC manual for further information.

TAPIR

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.

Executables

The ./analysis folder contains multiple potentially useful executables, including a tools for high throughput targeted proteomics data analysis (such as SWATH-MS data analysis). See the TRIC manual for further information on the TRIC alignment tool.

Documentation

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