{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/deep-learning-enables-de-novo-peptide","title":"Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry","arxiv_id":null,"date":"2018-12-20","proceeding":"Nature Methods 2018 12","authors":["Ngoc Hieu Tran","Rui Qiao","Lei Xin","Xin Chen","Chuyi Liu","Xianglilan Zhang","Baozhen Shan","Ali Ghodsi","Ming Li"],"abstract":"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.","url_abs":"https://www.nature.com/articles/s41592-018-0260-3","url_pdf":"https://www.nature.com/articles/s41592-018-0260-3.epdf?no_publisher_access=1&r3_referer=nature","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"deep-learning-enables-de-novo-peptide","repo_url":"https://github.com/nh2tran/DeepNovo-DIA","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"tf","reach":null}],"tasks":[{"task_slug":"de-novo-peptide-sequencing","task_name":"de novo peptide sequencing"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}