pXg: Comprehensive and Reliable Identification of MHC-I Antigens Using De Novo Peptide Sequencing and Immunotranscriptomic Datasets

peer-reviewed · Methods in Molecular Biology · 2026

peer-reviewed · Methods in Molecular Biology · 2026. Seunghyuk Choi et al. De novo peptide sequencing enables the identification of a broad repertoire of major histocompatibility…
Date 2026-10-16
Type peer-reviewed
Venue Methods in Molecular Biology
Publisher Springer US
Contribution downstream-application
DOI 10.1007/978-1-0716-5519-1_16
Citations (OpenAlex) 0
Venue 2-year citedness 1.14

Abstract

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.

Authors

  1. Seunghyuk Choi · Hanyang University, Kookmin University
  2. Shanji Zhang · Hanyang University
  3. Eunok Paek · Hanyang University, University of Seoul

Methods and tools

  • pXg: MHC-I noncanonical peptides

Methods it uses

Cites (12)

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