This program is deprecated in favor of https://github.com/mobiusklein/glycresoft_desktop, which wraps the application server in https://github.com/mobiusklein/glycresoft_app to run https://github.com/mobiusklein/glycan_profiling
This is a complete re-write of the GlycReSoft glycomics and glycoproteomics pipeline in Python
. It is suffixed _sqlalchemy
to reflect the fact that the majority of its data model is implemented using the SQLAlchemy database toolkit.
The pipeline was redesigned to be platform-agnostic.
- Combinatorial Naive Hypotheses
- Data-Driven Hypotheses
- LC-MS Profiling/Database Search
- LC-MS/MS Sequence Database Search
We implement an algorithm for constructing combinatorial hypotheses from simple composition rules for glycans and combinations for N-Linked glycopeptides.
We also provide an interface to glycomics databases such as Glycome-DB and GlyTouCan for constructing large naive hypotheses using the glypy library.
We provide a framework for building refined glycopeptide hypotheses from proteomics and/or glycomics experimental results.
Proteomics results in mzIdentML 1.1
format provide a definition for modified peptide sequences and proteins.