دورية أكاديمية
OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.
| العنوان: | OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases. |
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| المؤلفون: | Guilloy N; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Montreal, Québec H2X 3Y7, Canada., Brunet MA; Department of Pediatrics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada., Leblanc S; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Montreal, Québec H2X 3Y7, Canada., Jacques JF; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Montreal, Québec H2X 3Y7, Canada., Hardy MP; Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec H3C 3J7, Canada., Ehx G; Interdisciplinary Cluster for Applied Geno-Proteomics (GIGA-I3), University of Liège, Liège B-4000, Belgium., Lanoix J; Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec H3C 3J7, Canada., Thibault P; Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec H3C 3J7, Canada., Perreault C; Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec H3C 3J7, Canada.; Department of Medicine, Université de Montréal, Montreal, Québec H3C 3J7, Canada., Roucou X; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Montreal, Québec H2X 3Y7, Canada. |
| المصدر: | Journal of proteome research [J Proteome Res] 2023 May 05; Vol. 22 (5), pp. 1492-1500. Date of Electronic Publication: 2023 Mar 24. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Washington, D.C. : American Chemical Society, c2002- |
| مواضيع طبية MeSH: | Proteomics*/methods , Proteins*/genetics, Humans ; Databases, Protein ; Open Reading Frames ; Peptides/genetics ; Peptides/analysis |
| مستخلص: | Proteomic diversity in biological samples can be characterized by mass spectrometry (MS)-based proteomics using customized protein databases generated from sets of transcripts previously detected by RNA-seq. This diversity has only been increased by the recent discovery that many translated alternative open reading frames rest unannotated at unsuspected locations of mRNAs and ncRNAs. These novel protein products, termed alternative proteins, have been left out of all previous custom database generation tools. Consequently, genetic variations that impact alternative open reading frames and variant peptides from their translated proteins are not detectable with current computational workflows. To fill this gap, we present OpenCustomDB, a bioinformatics tool that uses sample-specific RNaseq data to identify genomic variants in canonical and alternative open reading frames, allowing for more than one coding region per transcript. In a test reanalysis of a cohort of 16 patients with acute myeloid leukemia, 5666 peptides from alternative proteins were detected, including 201 variant peptides. We also observed that a significant fraction of peptide-spectrum matches previously assigned to peptides from canonical proteins got better scores when reassigned to peptides from alternative proteins. Custom protein libraries that include sample-specific sequence variations of all possible open reading frames are promising contributions to the development of proteomics and precision medicine. The raw and processed proteomics data presented in this study can be found in PRIDE repository with accession number PXD029240. |
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| فهرسة مساهمة: | Keywords: alternative ORFs; alternative proteins; database; multicoding; precision medicine; proteogenomics; variants |
| المشرفين على المادة: | 0 (Proteins) 0 (Peptides) |
| تواريخ الأحداث: | Date Created: 20230324 Date Completed: 20230508 Latest Revision: 20230526 |
| رمز التحديث: | 20230527 |
| مُعرف محوري في PubMed: | PMC10167680 |
| DOI: | 10.1021/acs.jproteome.3c00054 |
| PMID: | 36961377 |
| قاعدة البيانات: | MEDLINE |
Find this issue from the American Chemical Society | تدمد: | 1535-3907 |
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| DOI: | 10.1021/acs.jproteome.3c00054 |