GproDIA is a pipeline for characterization of intact glycopeptides from DIA data with comprehensive statistical control.
The following software are required:
- Python (version 3.5.6 or later, Anaconda distribution is recommended)
- OpenSWATH (version 2.6.0)
- PyProphet (version 2.1.5)
- msproteomicstools (version 0.11.0)
- pGlyco (version 2.2.2 or later)
- MSConvert in ProteoWizard
GproDIA requires the following Python packages integrated in Anaconda:
- numpy (version 1.18.5)
- pandas (version 0.25.3)
- scipy (version 1.4.1)
- scikit-learn (version 0.22.2.post1)
Later versions may be compatible, but have not been tested.
Tutorials are avaliable in the docs folder.
GproDIA Tutorial: Getting Started describes the analysis workflow for a fission yeast dataset.
GproDIA Tutorial: Glycoform Inference describes a complete analysis workflow including glycoform inference for a serum dataset.
GproDIA Tutorial: Using Repository-Scale Library describes the analysis workflow for the serum dataset ultilizing a organism-specific repository of MS/MS spectra.
GproDIA Tutorial: Using Semi-Empirical Library describes the analysis workflow for the serum dataset with extended library coverage by generating semi-empirical library spectra.
Yang, Y., Yan, G., Kong, S., Wu, M., Yang, P., Cao, W., Qiao, L. GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control. Nat Commun 12, 6073 (2021). https://doi.org/10.1038/s41467-021-26246-3
GproDIA is distributed under a BSD license. See the LICENSE file for details.
Please report any problems directly to the github issue tracker. Also, you can send feedback to [email protected].