Deep Learning Based MS2 Feature Detection for Data-Independent Shotgun Proteomics

Accuracy of peptide identification in LC-MS analysis is crucial for information regarding the aspects of proteins that aid in biomarker discovery and the profiling of complex proteomes. The detection of peptide fragment ions in tandem mass spectrometry is still challenging given that current tools were not created or tested for the low-abundance, low-peak fragments of peptides found in MS2 data. Feature detection, a crucial pre-processing step in the LC-MS analysis pipeline that quantifies peptides by their mass-to-charge ratio, retention time, and intensity, is particularly challenging due to the overlapping nature of peptides and weak signals that are often indistinguishable from noises, thus creating a reliance on rigid mathematical structures and heuristics. In this study, we developed a deep-learning-based model with an innovative sliding window process that enables high-resolution processing of quantitative MS/MS data to conduct MS2 feature detection. Experimental results show that our model can produce more accurate values and identifications than existing feature detection tools, as well as a high rate of true positive features quantified. Therefore, we believe that our model illustrates the advantages of deep learning techniques applied towards computational proteomics.