2024 Volume 9 Issue 1 Pages 21-32
Multiomics/proteogenomics was developed through the integration of deep sequencing technology and mass spectrometry technology, which has expanded the search space for mass spectrometry data. Expanded landscapes for peptide searches work well with the enlarged data size acquired by state-of-the-art MS instruments. To accommodate this landscape, researchers have synergistically developed supporting algorithms to perform efficient peptide searches with machine learning, further advancing the multidisciplinary field of MS-associated omics. The utility of immunopeptidomics in the field of cancer immunology has been acknowledged in recent years, and this analytical field has benefited the most from innovations in MS technology. Along with the technological innovations of MS described above, fractionation techniques based on ion mobility have been developed to analyze delicate analytes, such as immunopeptides; in addition, clinical immunopeptidomics is being advanced to improve the efficacy of precision cancer immunotherapy.
In this review, we first outline the background and current status of immunopeptidomics research. Then, by introducing the differential ion mobility system in our laboratory, we explain why ion mobility is advantageous for immunopeptidomics analysis. For researchers that are new to this field or interested in immunopeptidomics, we also discuss frequently asked questions regarding sample preparation, MS parameters for immunopeptidomics (including differential ion mobility), and validation of the identified peptides as immunopeptides.
