دورية أكاديمية
Enhanced protein isoform characterization through long-read proteogenomics
| العنوان: | Enhanced protein isoform characterization through long-read proteogenomics |
|---|---|
| المؤلفون: | Rachel M. Miller, Ben T. Jordan, Madison M. Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou, Simi Kaur, Robert J. Millikin, Yunxiang Dai, Simone Tiberi, Peter J. Castaldi, Michael R. Shortreed, Chance John Luckey, Ana Conesa, Lloyd M. Smith, Anne Deslattes Mays, Gloria M. Sheynkman |
| المساهمون: | Rachel M. Miller, Ben T. Jordan, Madison M. Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou, Simi Kaur, Robert J. Millikin, Yunxiang Dai, Simone Tiberi, Peter J. Castaldi, Michael R. Shortreed, Chance John Luckey, Ana Conesa, Lloyd M. Smith, Anne Deslattes Mays, Gloria M. Sheynkman |
| سنة النشر: | 2022 |
| المجموعة: | IRIS Università degli Studi di Bologna (CRIS - Current Research Information System) |
| مصطلحات موضوعية: | Long-read RNA-seq, PacBio, Mass spectrometry-based proteomics, Protein inference, Proteogenomics, Nextflow, Lifebit CloudOS, Alternative splicing, SQANTI, Iso-Seq |
| الوصف: | Background: The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) provides full-length transcripts which can be used to predict full-length protein isoforms. Results: We describe here a long-read proteogenomics approach for integrating sample-matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data to enable detection of protein isoforms previously intractable to MS-based detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis. Conclusions: Our work suggests that the incorporation of long-read sequencing and proteomic data can facilitate improved characterization of human protein isoform diversity. Our first-generation pipeline provides a strong foundation for future development of long-read proteogenomics and its adoption for both basic and translational research. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | ELETTRONICO |
| اللغة: | English |
| العلاقة: | info:eu-repo/semantics/altIdentifier/pmid/35241129; info:eu-repo/semantics/altIdentifier/wos/WOS:000764049100002; volume:23; issue:1; firstpage:1; lastpage:28; numberofpages:28; journal:GENOME BIOLOGY; https://hdl.handle.net/11585/949883Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85125692178; https://doi.org/10.1186/s13059-022-02624-yTest |
| DOI: | 10.1186/s13059-022-02624-y |
| الإتاحة: | https://doi.org/10.1186/s13059-022-02624-yTest https://hdl.handle.net/11585/949883Test |
| حقوق: | info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.4D439E24 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1186/s13059-022-02624-y |
|---|