Intensity and retention time prediction improves the rescoring of protein ‐nucleic acid cross‐links

AbstractIn 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.

Source: Proteomics - April 17, 2024 Category: Biochemistry Authors: Arslan Siraj, Robbin Bouwmeester, Arthur Declercq, Luisa Welp, Aleksandar Chernev, Alexander Wulf, Henning Urlaub, Lennart Martens, Sven Degroeve, Oliver Kohlbacher, Timo Sachsenberg Tags: RESEARCH ARTICLE Source Type: research