🇦🇺 Glycoscientist
4/6 GlycoShape (https://glycoshape.org) is an OA database and toolbox that allows you to restore the 3D structure of glycoproteins with a fast and accurate algorithm named Re-Glyco.
The database counts > 550 glycans to date, largely from the human glycome with examples from all species. For an overview check out the figure below ⬇️
"Wait, I thought you lived in South Africa!" Well, yes, but then we ran into a bit of a challenge.
If you would like to know more about how we decided to come to the #Netherlands this blog post is for you!
https://pickingupthetabb.wordpress.com/2024/10/12/a-peripatetic-proteomics-professional/
Slightly delayed due to my holidays, but excited to share this new paper that came out online a little while ago in ACS Applied Materials and Interfaces: https://doi.org/10.1021/acsami.4c08428 In it, PhD student Pushpa Rampratap spearheaded our effort to use MAS #NMR to study ECM-like #hydrogels. In a prior publication (https://doi.org/10.1016/j.carbpol.2023.121063) she described methods for preparing 13C enriched version of the polysaccharide hyaluronic acid…. #glycotime #nmrchat #ssnmr
@Elisa Any AGS drinks tonight?
Having a great time on the last day of #IMSC2024 some fantastic #teammassspec work on environmental pollution and space geochemistry this morning. Plus a small plug for a great conference next year. #AusOmics
In this month's interesting fact about #glyco we learn how #monosaccharides not synthesized by humans/mammals could occur as part of the human/mammalian glycan repertoire.
For more interesting facts check: https://research.bidmc.org/ncfg/interestingfacts/interesting-facts-about-glycans
@RonBeavis Much of the major vendor’s user meetings are recorded, and even live streamed. Much better for remote attendees.
A spoonful of sugar #11 🍬
As the rest of the community, we are excited about #AF3 and have been testing its performance in the reconstruction of glycans and glycosylation. We have found the following limitations users should be aware of:
- The structure of the Asn-linkages is incorrect
- All N-glycans have an a2 arm, while the Man should be in a3
What we suggest 😜 is to build the protein with AF3 and to reglycosylate it with ReGlyco at https://glycoshape.org :awesome:
Excellent review by Pamela Stanley @NatureRevGenet
about genetics of glycosylation. Must-read!
Is this just my OCD, or is this ASMR for mass spectrometrists?
No noise is good noise.
Human Rh associated glycoprotein (RHAG): HPA cell type mRNA distribution + GPMDB cell type protein tabbulation & PeptideAtlas tissue/cell type protein distribution. #proteomics
Weights for the non-enzymatic version of Casanovo v4.x are now available. Use this to analyze data that was generated using a different protease than trypsin, for immunopeptidomics, ...
You can find the model weights on GitHub under the "Assets" of release v4.0.0: https://github.com/Noble-Lab/casanovo/releases/tag/v4.0.0
Note that by default Casanovo will automatically download the tryptic model weights. To use the non-enzymatic model, download the weights file manually and specify it using the `--model` command-line argument.
@Elisa I’m trying to unravel the meaning of this toot, but we need improved analytical methodology to decipher the mechanisms involved.
New update to GlyCosmos has been released with new data for lectins, glycan species and updated glycan search functionality! See glycosmos.org/release for details. #glycotime
@RonBeavis @pwilmart I think I count as a later wave then, forensic science/biotech background rather than physics/physical chemistry. Though I’ve had to learn a lot on the fly, and continue to do so.
@pwilmart @RonBeavis
It was a guess, but the tooth expression of AMEX was enough to rule it out.
It’s the most wonderful #glycotime of the year!! 🤩 🥳
Let us introduce you to #GlycoShape (https://glycoshape.org and #bioRxiv link below), a web platform that allows users to restore glycoproteins 3D structures (PDB, AF/RoseTTAFold or own) to their natural, functional state by adding the missing glycan structures. #bioRxiv ⬇️ tootorial🧵 1/8
https://doi.org/10.1101/2023.12.11.571101
@RonBeavis
Bulky steric hindrance to reduce protease susceptibility?
@RonBeavis
Do you think this is the result of the constant measuring contests of trying to get the highest number of protein IDs in a given amount of time?
Theoretically, the peptides should be able to elute from C18.
