glycogenius

GlycoGenius - Glycomics Data Analysis Tool

GlycoGenius is a python script that aims to be an all-in-one solution for data analysis of N- and O-glycomics full scan or DDA data.

Glycobiologists analyzing glycans' mass spectrometer data usually rely on several different tools to perform different tasks on different parts of their workflow and, in between the use of all those different tools, there's usually a lot of manual work that has to be done at least for data curating.

With that in mind, this tool aims to put all the usual workflow for glycomics in a single place.

In order to do that, this tool is able to do several different tasks automatically:

• Create glycans libraries based on user input, which can be monosaccharides numbers or specific glycans;
• Automatically identify noise level in samples;
• Process the spectra data and creates refined extracted ion chromatograms (EICs) for each glycan analyzed;
• Peak-pick multiple peaks in a single EIC, which allows the identification and possibly quantification of plausible isomers;
• Provide scorings of isotopic distribution peaks and chromatogram peak curve fitting based on relation and correlation;
• Identify PPM differences between theoretical mass and identified mz;
• Calculate signal-to-noise ratio;
• Identify MS2 glycans' fragments and assign them to its respective precursor;
• And much more!

Installation

There are two ways to install it:

1. Download the latest version of the Graphical User Interface from Releases page on https://github.com/LoponteHF/GlycoGenius_GUI, unzip it and run the executable file (Windows only, for other OS, you can install the GUI from PyPI);
2. Install from PyPI:
   1. Install Python from python.org or from your OS package distributor;
   2. Type "pip install glycogenius" on a terminal

Usage

1. Export your MS data to an MzXML or MzML file;
2. Type 'glycogenius' in the terminal;

		glycogenius

1. Follow instructions:
   • You can analyze directly on the CLI;
   • You can export a parameters file for advanced executions;
2. If you exported the parameters file, pipeline it to glycogenius after setting it up.
   • ie. in terminal type:

        cat .\glycogenius_parameters.ini | glycogenius

Citation

Article for citation currently being finished.

Credits

Pyteomics:

Goloborodko, A.A.; Levitsky, L.I.; Ivanov, M.V.; and Gorshkov, M.V. (2013) “Pyteomics - a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics”, Journal of The American Society for Mass Spectrometry, 24(2), 301–304. DOI: 10.1007/s13361-012-0516-6

Levitsky, L.I.; Klein, J.; Ivanov, M.V.; and Gorshkov, M.V. (2018) “Pyteomics 4.0: five years of development of a Python proteomics framework”, Journal of Proteome Research. DOI: 10.1021/acs.jproteome.8b00717

Dill for Python:

M.M. McKerns, L. Strand, T. Sullivan, A. Fang, M.A.G. Aivazis, "Building a framework for predictive science", Proceedings of the 10th Python in Science Conference, 2011; http://arxiv.org/pdf/1202.1056

Michael McKerns and Michael Aivazis, "pathos: a framework for heterogeneous computing", 2010- ; https://uqfoundation.github.io/project/pathos

Numpy:

Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020). DOI: 10.1038/s41586-020-2649-2.

SciPy:

Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Eric Jones, Robert Kern, Eric Larson, CJ Carey, İlhan Polat, Yu Feng, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Ian Henriksen, E.A. Quintero, Charles R Harris, Anne M. Archibald, Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt, and SciPy 1.0 Contributors. (2020) SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nature Methods, 17(3), 261-272.

Whittaker-Eilers smoothing implementation:

P. H. C. Eilers, "A perfect smoother", Anal. Chem. 2003, 75, 3631-3636

J. Midelet, A. H. El-Sagheer, T. Brown, A. G. Kanaras, A. Débarre, M. H. V. Werts, "Spectroscopic and Hydrodynamic Characterisation of DNA-Linked Gold Nanoparticle Dimers in Solution using Two-Photon Photoluminescence", ChemPhysChem 2018, 19, 827.

Pandas:

The pandas development team, Pandas, Zenoddo, Feb 2020, DOI:10.5281/zenodo.3509134

Logo/Banner Image:

Based on an image generated by Bing Copilot (powered by DALL-E 3)

License

This project is licensed under GNU GPLv3 or later