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.