Comparing Machine Learning Architectures for the Prediction of Peptide Collisional Cross Section

1Mass spectrometry is the method of choice in large-scale proteomics studies. One common method is data-independent acquisition (DIA), which allows for high-throughput analysis of biological samples, but also produces complex data. Methods of peptide separation, in addition to retention time, improve data analysis and there has been increasing interest in separating peptides based on collisional cross section (CCS), which is a measure of the size of a peptide. However, existing libraries that are used during data analysis lack CCS measurements, and this data is expensive and time-consuming to acquire. This has led to the desire to predict library values for mass spectrometry analysis. Here we compare three deep learning architectures, LSTM, CNN, and transformer, for the tasks of retention time and collisional cross section prediction. We show that the LSTM and CNN models perform similarly and that the transformer has a lower performance than expected.