The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts
As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library cons...
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| Format: | Article |
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MDPI AG
2020-05-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/9/5/104 |
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| author | Cary Pirone-Davies Melinda A. McFarland Christine H. Parker Yoko Adachi Timothy R. Croley |
| author_facet | Cary Pirone-Davies Melinda A. McFarland Christine H. Parker Yoko Adachi Timothy R. Croley |
| author_sort | Cary Pirone-Davies |
| collection | DOAJ |
| description | As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with <i>Juglans regia</i>, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography–mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156–1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms. |
| first_indexed | 2024-03-10T19:44:09Z |
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| id | doaj.art-cb51da68b20a47dc84e240da23e2629b |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T19:44:09Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-cb51da68b20a47dc84e240da23e2629b2023-11-20T00:59:02ZengMDPI AGBiology2079-77372020-05-019510410.3390/biology9050104The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree NutsCary Pirone-Davies0Melinda A. McFarland1Christine H. Parker2Yoko Adachi3Timothy R. Croley4Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USAOffice of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USAOffice of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USAOffice of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USAOffice of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USAAs the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with <i>Juglans regia</i>, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography–mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156–1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms.https://www.mdpi.com/2079-7737/9/5/104nut allergenwalnutpecan<i>Juglans regia</i>de-novo transcriptomeproteomics |
| spellingShingle | Cary Pirone-Davies Melinda A. McFarland Christine H. Parker Yoko Adachi Timothy R. Croley The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts Biology nut allergen walnut pecan <i>Juglans regia</i> de-novo transcriptome proteomics |
| title | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
| title_full | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
| title_fullStr | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
| title_full_unstemmed | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
| title_short | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
| title_sort | utility of genomic and transcriptomic data in the construction of proxy protein sequence databases for unsequenced tree nuts |
| topic | nut allergen walnut pecan <i>Juglans regia</i> de-novo transcriptome proteomics |
| url | https://www.mdpi.com/2079-7737/9/5/104 |
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