دورية أكاديمية
PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models.
| العنوان: | PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models. |
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| المؤلفون: | Petrovskiy DV; Institute of Biomedical Chemistry, 119121, Moscow, Russia., Nikolsky KS; Institute of Biomedical Chemistry, 119121, Moscow, Russia., Kulikova LI; Institute of Biomedical Chemistry, 119121, Moscow, Russia., Rudnev VR; Institute of Biomedical Chemistry, 119121, Moscow, Russia., Butkova TV; Institute of Biomedical Chemistry, 119121, Moscow, Russia., Malsagova KA; Institute of Biomedical Chemistry, 119121, Moscow, Russia., Kopylov AT; Institute of Biomedical Chemistry, 119121, Moscow, Russia., Kaysheva AL; Institute of Biomedical Chemistry, 119121, Moscow, Russia. kaysheva1@gmail.com. |
| المصدر: | Scientific reports [Sci Rep] 2024 Jul 01; Vol. 14 (1), pp. 15000. Date of Electronic Publication: 2024 Jul 01. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : Nature Publishing Group, copyright 2011- |
| مواضيع طبية MeSH: | Tandem Mass Spectrometry*/methods , Sequence Analysis, Protein*/methods , Peptides*/chemistry , Peptides*/analysis, Amino Acid Sequence ; Software ; Proteomics/methods ; Algorithms |
| مستخلص: | The primary objective of analyzing the data obtained in a mass spectrometry-based proteomic experiment is peptide and protein identification, or correct assignment of the tandem mass spectrum to one amino acid sequence. Comparison of empirical fragment spectra with the theoretical predicted one or matching with the collected spectra library are commonly accepted strategies of proteins identification and defining of their amino acid sequences. Although these approaches are widely used and are appreciably efficient for the well-characterized model organisms or measured proteins, they cannot detect novel peptide sequences that have not been previously annotated or are rare. This study presents PowerNovo tool for de novo sequencing of proteins using tandem mass spectra acquired in a variety of types of mass analyzers and different fragmentation techniques. PowerNovo involves an ensemble of models for peptide sequencing: model for detecting regularities in tandem mass spectra, precursors, and fragment ions and a natural language processing model, which has a function of peptide sequence quality assessment and helps with reconstruction of noisy sequences. The results of testing showed that the performance of PowerNovo is comparable and even better than widely utilized PointNovo, DeepNovo, Casanovo, and Novor packages. Also, PowerNovo provides complete cycle of processing (pipeline) of mass spectrometry data and, along with predicting the peptide sequence, involves the peptide assembly and protein inference blocks. (© 2024. The Author(s).) |
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| معلومات مُعتمدة: | 122092200056-9 Russian Federation Fundamental Research Program for the long-term period for 2021-2030 |
| المشرفين على المادة: | 0 (Peptides) |
| تواريخ الأحداث: | Date Created: 20240701 Date Completed: 20240702 Latest Revision: 20240704 |
| رمز التحديث: | 20240704 |
| مُعرف محوري في PubMed: | PMC11217302 |
| DOI: | 10.1038/s41598-024-65861-0 |
| PMID: | 38951578 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 2045-2322 |
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| DOI: | 10.1038/s41598-024-65861-0 |