We present DeepNovo-DIA, a de novo peptide-sequencing method for data-independent acquisition (DIA) mass spectrometry data. We use neural networks to capture precursor and fragment ions across m/z, retention-time, and intensity dimensions. They are then further integrated with peptide sequence patterns to address the problem of highly multiplexed spectra. DIA coupled with de novo sequencing allowed us to identify novel peptides in human antibodies and antigens.
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This work was funded in part by NSERC (grant OGP0046506), China’s Research and Development Program (grants 2016YFB1000902 and 2018YFB1003202), the NSFC (grant 61832019), and the Canada Research Chair program for M.L. N.H.T. was supported by the Mitacs Elevate Fellowship. The authors thank N. Keshav, K.P. Choi, and K. Xiong for discussions and proofreading of the manuscript.
L.X., X.C., and B.S. are employees of Bioinformatics Solutions Inc., Waterloo, Ontario, Canada.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Integrated supplementary information
Supplementary Figure 1 Comparison of unique peptides identified by DeepNovo, PECAN, and Spectronaut from the plasma dataset.
Note that the number of 3,268 de novo peptides reported here by DeepNovo have yet been validated (see Supplementary Note 1)
Distribution of de novo confidence score versus peptide abundance of all peptides reported by DeepNovo from the plasma dataset
Distribution of retention times of 1,143 de novo peptides reported by DeepNovo and database peptides reported by PECAN and Spectronaut from the plasma dataset
Distribution of amino acids of 1,143 de novo peptides reported by DeepNovo and database peptides reported by PECAN and Spectronaut from the plasma dataset
Supplementary Figure 5 Unique peptides identified by DeepNovo, PECAN, and Spectronaut from the plasma dataset.
(a) Original model trained with the urine dataset. (b) Model retrained with part of the plasma dataset. Note that we have removed from DeepNovo the features that were used to retrain the model, so the numbers of DeepNovo peptides in a are less than those reported in Supplementary Fig. 1. DeepNovo peptides have not been filtered by sequencing errors and augmented database search (see Supplementary Note 1)
Example of three de novo peptides aligned to the variable region of a recently published human antibody for malaria vaccine design
Unique peptides identified by DeepNovo, OpenSWATH, and Spectronaut from the dataset Jurkat-Oxford
Abundance distribution of 130 de novo peptides versus 102 peptides identified by DeepNovo and OpenSWATH or Spectronaut from the dataset Jurkat-Oxford
DeepNovo sequencing framework
Supplementary Figures 1–11 and Supplementary Notes 1 and 2
Documentation for using DeepNovo
Scripts and Swiss-Prot database FASTA file
Examples of DIA spectra from the plasma dataset that contain multiple precursors with at least one low-abundance, novel peptide identified by DeepNovo but not by other database search tools
Twelve examples from the plasma dataset showing that the low-abundance, novel peptides identified by DeepNovo have better supporting fragment ions than those candidate sequences returned by the database search engine
Evidence of supporting fragment ions (left column), coelution profiles of fragment ions and precursor ion (right column), and antibody protein ID for 30 low-abundance, novel peptides identified by DeepNovo from the plasma dataset. The database search engine was not able to find any candidate sequences that matched these 30 precursors
Twelve examples of low-abundance, novel HLA peptides that were identified by DeepNovo but not by other database search tools
Summary of training and testing datasets in our study
List of 2,753 unique peptides predicted by DeepNovo from the plasma dataset
Novel peptides that were identified by DeepNovo from the plasma dataset and were found in variable regions of human immunoglobulin light chains
Novel peptides that were identified by DeepNovo from the plasma dataset and were found in variable regions of human immunoglobulin heavy chains
Novel peptides that were identified by DeepNovo from the plasma dataset and contained human natural variants
List of 304 unique peptides predicted by DeepNovo from the Jurkat-Oxford dataset
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Tran, N.H., Qiao, R., Xin, L. et al. Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry. Nat Methods 16, 63–66 (2019). https://doi.org/10.1038/s41592-018-0260-3
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