Haixu Tang (left) and Yuzhen Ye
Haixu Tang and Yuzhen Ye, both professors of informatics and computer science at the Luddy School of Informatics, Computing, and Engineering, have been awarded a grant worth more than $780,000 from the National Science Foundation to improve machine learning algorithms via deep learning techniques for peptide tandem mass spectra prediction.
Peptides are segments of proteins between 2-30 amino acids long, and often used to identify proteins in high-throughput proteomics experiments. The ability to predict peptide tandem mass spectra prediction can significantly enhance the understanding of peptide fragmentation mechanisms in mass spectrometry and improve peptide identification in proteomics. Tang and Ye have previously used artificial intelligence techniques to predict tandem mass spectra of unmodified peptides.
“This NSF grant will allow us to extend our approaches to peptides with post-translational modifications,” Tang said. “It will also allow us to explore the application of deep learning algorithms for predicting other peptide properties, such as elution time and ion mobility, while also exploring the application of the next generation of AI techniques to scientific problems, which is a new direction we hope to pursue.”
Tang and Ye have been working on peptide tandem mass spectra prediction for the past 15 years, and the rapid advance of deep learning techniques has allowed the team to make positive progress. They plan on leveraging the strength of the Luddy School in AI, including the future opening of the Luddy Center for Artificial Intelligence, to conduct a full-spectrum prediction of peptide tandem mass spectra for the first time.
“This grant will give us the chance to broaden the impact of the next generation of AI,” Tang said.
The deep learning approaches developed in the study can also be applied to the prediction of other biochemical properties of peptides.
“Artificial intelligence will help us explore so many unknowns as the technology and our research advances,” said Kay Connelly, the associate dean for research at the Luddy School. “This grant and the work being conducted by Haixu and Yuzhen will help push the boundary of what is possible, and it will set a foundation for future developments.”