Intensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links.
Proteomics
; 24(8): e2300144, 2024 Apr.
Article
in En
| MEDLINE
| ID: mdl-38629965
ABSTRACT
In protein-RNA cross-linking mass spectrometry, UV or chemical cross-linking introduces stable bonds between amino acids and nucleic acids in protein-RNA complexes that are then analyzed and detected in mass spectra. This analytical tool delivers valuable information about RNA-protein interactions and RNA docking sites in proteins, both in vitro and in vivo. The identification of cross-linked peptides with oligonucleotides of different length leads to a combinatorial increase in search space. We demonstrate that the peptide retention time prediction tasks can be transferred to the task of cross-linked peptide retention time prediction using a simple amino acid composition encoding, yielding improved identification rates when the prediction error is included in rescoring. For the more challenging task of including fragment intensity prediction of cross-linked peptides in the rescoring, we obtain, on average, a similar improvement. Further improvement in the encoding and fine-tuning of retention time and intensity prediction models might lead to further gains, and merit further research.
Key words
Full text:
1
Database:
MEDLINE
Main subject:
Nucleic Acids
Language:
En
Year:
2024
Type:
Article