ReNovo: Retrieval-Based De Novo Mass Spectrometry Peptide Sequencing

Proteomics is the large-scale study of proteins. Tandem mass spectrometry, as the only high-throughput technique for protein sequence identification, plays a pivotal role in proteomics research. One of the long-standing challenges in this field is peptide identification, which entails determining the specific peptide (sequence of amino acids) that corresponds to each observed mass spectrum. The conventional approach involves database searching, wherein the observed mass spectrum is scored against a pre-constructed peptide database. However, the reliance on pre-existing databases limits applicability in scenarios where the peptide is absent from existing databases. Such circumstances necessitate de novo peptide sequencing, which derives peptide sequence solely from input mass spectrum, independent of any peptide database. Despite ongoing advancements in de novo peptide sequencing, its performance still has considerable room for improvement, which limits its application in large-scale experiments. In this study, we introduce a novel Retrieval-based De Novo peptide sequencing methodology, termed ReNovo, which draws inspiration from database search methods. Specifically, by constructing a datastore from training data, ReNovo can retrieve information from the datastore during the inference stage to conduct retrieval-based inference, thereby achieving improved performance. This innovative approach enables ReNovo to effectively combine the strengths of both methods: utilizing the assistance of the datastore while also being capable of predicting novel peptides that are not present in pre-existing databases. A series of experiments have confirmed that ReNovo outperforms state-of-the-art models across multiple widely-used datasets, incurring only minor storage and time consumption, representing a significant advancement in proteomics. Supplementary materials include the code.