دورية أكاديمية
Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry.
| العنوان: | Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry. |
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| المؤلفون: | Jorge GL; Sao Paulo State University, Department of Technology, Jaboticabal, Sao Paulo, Brazil. Electronic address: gabriel.lemes@unesp.br., Balbuena TS; Sao Paulo State University, Department of Technology, Jaboticabal, Sao Paulo, Brazil. Electronic address: tiago.balbuena@unesp.br. |
| المصدر: | Biochimica et biophysica acta. Proteins and proteomics [Biochim Biophys Acta Proteins Proteom] 2021 Mar; Vol. 1869 (3), pp. 140594. Date of Electronic Publication: 2020 Dec 29. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101731734 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-1454 (Electronic) Linking ISSN: 15709639 NLM ISO Abbreviation: Biochim Biophys Acta Proteins Proteom Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Amsterdam : Elsevier |
| مواضيع طبية MeSH: | Eucalyptus/*chemistry , Plant Proteins/*chemistry , Tandem Mass Spectrometry/*methods, Amino Acid Sequence ; Amino Acid Substitution ; Genomics/methods ; Proteomics/methods |
| مستخلص: | Eucalyptus species are widely used in the forestry industry, and a significant increase in the number of sequences available in database repositories has been observed for these species. In proteomics, a protein is identified by correlating the theoretical fragmentation spectrum derived from genomic/transcriptomic data against the experimental fragmentation mass spectrum acquired from large-scale analysis of protein mixtures. Proteogenomics is an alternative approach that can identify novel proteins encoded by regions previously considered as non-coding. This study aimed to confidently identify and confirm the existence of previously unknown protein-coding sequences in the Eucalyptus grandis genome. To this end, we used a modified spectral correlation strategy and a dedicated de novo peptide sequencing pipeline. Upon the strategy used here, we confidently identified 41 novel peptide forms and six peptides containing at least one single amino acid substitution. The most representative genomic class of novel peptides was identified as originating from alternative reading frames. In contrast, no clear single amino acid substitution pattern was identified. Validation of the identifications was carried out using a parallel reaction monitoring approach that provided further mass spectrometry support for the existence of the novel peptide sequences. Data are available via ProteomeXchange with identifier PXD022110. (Copyright © 2020 Elsevier B.V. All rights reserved.) |
| فهرسة مساهمة: | Keywords: Bottom-up proteomics; Parallel reaction monitoring; Proteogenomics; Proteomics |
| المشرفين على المادة: | 0 (Plant Proteins) |
| تواريخ الأحداث: | Date Created: 20210101 Date Completed: 20210719 Latest Revision: 20210719 |
| رمز التحديث: | 20231215 |
| DOI: | 10.1016/j.bbapap.2020.140594 |
| PMID: | 33385527 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1878-1454 |
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| DOI: | 10.1016/j.bbapap.2020.140594 |