#immunopeptidomics — Public Fediverse posts

Pipeline release! nf-core/mhcquant v3.2.0 - 3.2.0 - Solitude!
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Please see the changelog: https://github.com/nf-core/mhcquant/releases/tag/3.2.0

#dda #immunopeptidomics #massspectrometry #mhc #openms #peptides #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mhcquant v3.1.0 - 3.1.0 - BlüBa!
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Please see the changelog: https://github.com/nf-core/mhcquant/releases/tag/3.1.0

#dda #immunopeptidomics #massspectrometry #mhc #openms #peptides #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mhcquant v3.0.0 - MHCquant 3.0.0 - Monrepos!

Please see the changelog: https://github.com/nf-core/mhcquant/releases/tag/3.0.0

#dda #immunopeptidomics #massspectrometry #mhc #openms #peptides #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mhcquant v2.6.0 - MHCquant 2.6.0 - Mr Bob!

Please see the changelog: https://github.com/nf-core/mhcquant/releases/tag/2.6.0

#dda #immunopeptidomics #mass-spectrometry #mhc #openms #peptides #nfcore #openscience #nextflow #bioinformatics

From these MS/MS spectrum and PSM characteristics, can you guess whether it's #immunopeptidomics or #BottomUpProteomics data?

Join us in the #BioinformaticsHub at #HUPO2023 today to discuss #MachineLearning applications for immunopeptidomics data analysis.

Slides: https://doi.org/10.5281/zenodo.8353779
Notebook to generate the figures: https://gist.github.com/bittremieux/af2985306c4121ab70ac66f44398951c

Immunopeptidomics data analysis is very challenging:
- A massive search space has to be considered (all subsequences of the proteins under consideration).
- Immunopeptides have different characteristics than standard tryptic peptides (non-tryptic peptide termini, predominantly singly charged).

This leads to low spectrum annotation rates in #immunopeptidomics. 😥

Our work on fragment ion intensity prediction for the analysis of timsTOF #immunopeptidomics data is now online on #bioRxiv: https://www.biorxiv.org/content/10.1101/2023.07.17.549401v1

Check out this great effort by Charlotte Adams, who basically learned #DeepLearning/#MachineLearning from scratch for this project.

Thread. 👇

The slides from my presentation at the #BSPREUPA2023 conference on timsTOF fragment ion intensity prediction for #immunopeptidomics are available here: https://doi.org/10.5281/zenodo.8163554

Fantastic work by Charlotte Adams. Stay tuned for the full preprint very soon.