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glyXtoolMS

glyXtoolMS is a (semi-) automated software for the targeted analysis of glycopeptide mass spectrometry data, based on OpenMS. The user manual is available for download under https://github.com/glyXera/glyXtoolMS/blob/master/docs/glyXtoolMS%20User%20Guide.pdf

Getting Started

Prerequisites

In order to run glyXtoolMS a python 2.7.x envirunment and OpenMS have to be installed.

OpenMS

For installation of OpenMS visit https://www.openms.de/ and follow the download/install or build instructions for your operating system. After installation the following tools should be available: TOPPAS and TOPPView.

Python

To run glyXtoolMS, a python 2.7 installation is required, together with the package manager pip. The use of a virtual environment like virtualenvwrapper is recommended, to handle p

Install python 2.7 from https://www.python.org/. The package manager for python will then be installed, too. To check this, open a console and type the command β€œpip”. If it has not been installed, follow the installation instructions on https://pip.pypa.io/en/stable/installing/#do-i-need-to-install-pip.

The use of a virtual environment is recommended, in case multiple python installations with different package setups are installed on the computer. For the installation of virtualenvwrapper, please refer to https://virtualenvwrapper.readthedocs.io/en/latest/

Virtualenvwrapper can be installed via pip:

pip install virtualenvwrapper

afterwards a new environment can be created using:

mkvirtualenv <envname>

switch into the environment using:

workon <envname>

glyXtoolMS

glyXtoolMS can then be installed using pip:

pip install glyXtoolMS

The dependencies canvasvg, configparser, lxml ,numpy,pyopenms, pyperclip, and xlwt should then be automatically downloaded and installed.

alternatively the .egg or .wheel can be downloaded from https://test.pypi.org/project/glyxtoolms/

or build manually from www.github.com/mpioch/glyXtoolMS

After the installation of glyXtoolMS, the glyXtoolMS Evaluator should be acessable via the console command:

glyxtoolms

To complete the installation of TOPAS/glyXtoolMS the path to the OpenMS installation will be requested during the first run of glyXtoolMS and the necessary TOPPAS scripts will be copied to the OpenMS installation. Within this window, also newly downloaded TOPPAS workflows can be adapted to the new OpenMS script path.

Analysing the Example data sets

An example data set can be downloaded from PRIDE via https://www.ebi.ac.uk/pride/archive/projects/PXD009716 containing an human IgG and human fibrinogen mass spectrometry file, the N-glycan database, the FASTA files, the TOPPAS workflow,s and the resulting analysis files. The procedure for handling and analyzing the data file is detailed within the documentation.

Updated example workflows for fibrinogen and IgG (in case of changes in OpenMS and glyXtoolMS tools) are available under https://gist.github.com/mpioch/4e4beec032bc51c7e1c70528a916e13b and https://gist.github.com/mpioch/15bb44618bf837bfbdf007c237b29d89

Authors

  • Markus Pioch - Initial work - mpioch
  • Dr. Erdmann Rapp

License

This project is licensed under the GPL-3.0 License - see the LICENSE file for details

Acknowledgments

  • Alexander Behne
  • Terry Nguyen-Khuong
  • Stackoverflow

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🐍 Open-Source Software for the semi-automated analysis of glycopeptide mass spectrometry data

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