Examining and fine-tuning the selection of glycan compositions with GlyConnect Compozitor

Abstract

A key point in achieving accurate intact glycopeptide identification is the definition of the glycan composition file that is used to match experimental with theoretical masses by a glycoproteomics search engine. At present, these files are mainly built from searching the literature and/or querying data sources focused on posttranslational modifications. Most glycoproteomics search engines include a default composition file that is readily used when processing mass spectrometry data. We introduce here a glycan composition visualising and comparative tool associated with the GlyConnect database and called GlyConnect Compozitor.It has web interface through which the database can be queried to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarising information searched in the database. These results provide a guide for selecting or deselecting compositions in a file in order to reflect the context of a study as closely as possible. As part of the tool collection of the Glycomics@ExPASy initiative, Compozitor is hosted at https://glyconnect.expasy.org/compozitor/ where it can be run as a web application.It is also directly accessible from the GlyConnect database.

Improved N- and O-Glycopeptide Identification using High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS)

“…First, we performed a simple yet effective visualization of glycan compositions using the GlyConnect Compozitor 32 tool to correct the sparsity of missing compositions and identify potential outliers’ glycan clusters (Figure S3) . This step allowed us to confirm the ‘difficult-to-identify glycopeptide features such as NeuAc, NeuGc, and multi-Fuc that are often mis-annotated 33 and pass the empirical score.…”

“…In this work, the glycan database used for glycopeptide identification is limited to the default glycan compositions available in Byonic. Nevertheless, visualization of glycan compositions via GlyConnect Compozitor 32 enables the user to modify the glycan compositions and refine the search as required to reflect the context of the investigation. Notwithstanding, the logical next step would be to associate glycan composition-based visualization with every single glycopeptide detected to identify the outliers and increase confidence in glycopeptide identification.…”

Mammalian Milk Glycomes: Connecting the Dots between Evolutionary Conservation and Biosynthetic Pathways

“…Additionally, the identity of the involved enzymes is still incompletely understood, even in humans 4,7 . Therefore, we developed an empirical algorithm that does not rely on known enzymatic activities and that finds the minimum number of proposed intermediates to connect all observed structures in a biosynthetic network (see STAR Methods), conceptually vaguely related to the Compozitor framework 21 , yet not limited to compositions but also taking glycan structure into account. In this, glycans are conceptualized as nodes, connected by edges representing biosynthetic steps.…”