pXg: Comprehensive and Reliable Identification of MHC-I Antigens Using De Novo Peptide Sequencing and Immunotranscriptomic Datasets
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| Format: | Recurso digital |
| Language: | English |
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Zenodo
2025
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| _version_ | 1866902237757833216 |
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| author | Choi, Seunghyuk |
| author_facet | Choi, Seunghyuk |
| contents | <p>De novo peptide sequencing enables the identification of a broad repertoire of major histocompatibility complex class I-associated peptides, providing a valuable source of potential immunotherapeutic targets in cancer. Nevertheless, its practical utility remains limited by the absence of robust methods for confidently determining peptide-spectrum matches and interpreting their proteogenomic information. This chapter presents the pXg workflow, designed to comprehensively and reliably identify peptides derived from de novo sequencing in mass spectrometry-based immunopeptidomics, integrated with matched RNA-seq data. We guide the reader through the use of pXg, covering the rescoring of peptide-spectrum matches and the estimation of a false discovery rate from the popular de novo sequencing tool Casanovo. This ultimately yields rich proteogenomic insights into the identified peptides.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17042919 |
| institution | Zenodo |
| language | eng |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | pXg: Comprehensive and Reliable Identification of MHC-I Antigens Using De Novo Peptide Sequencing and Immunotranscriptomic Datasets Choi, Seunghyuk <p>De novo peptide sequencing enables the identification of a broad repertoire of major histocompatibility complex class I-associated peptides, providing a valuable source of potential immunotherapeutic targets in cancer. Nevertheless, its practical utility remains limited by the absence of robust methods for confidently determining peptide-spectrum matches and interpreting their proteogenomic information. This chapter presents the pXg workflow, designed to comprehensively and reliably identify peptides derived from de novo sequencing in mass spectrometry-based immunopeptidomics, integrated with matched RNA-seq data. We guide the reader through the use of pXg, covering the rescoring of peptide-spectrum matches and the estimation of a false discovery rate from the popular de novo sequencing tool Casanovo. This ultimately yields rich proteogenomic insights into the identified peptides.</p> |
| title | pXg: Comprehensive and Reliable Identification of MHC-I Antigens Using De Novo Peptide Sequencing and Immunotranscriptomic Datasets |
| url | https://doi.org/10.5281/zenodo.17042919 |