• Investigating mass spectrometry methods in identifying neoantigens and its application in designing personalized cancer vaccines
  • Mehdi Niajalili,1 Hassan Salehipour Masooleh,2,* Parsa Sharifi Visheh sarayi,3
    1. Department of Mechanical Engineering, Technical and Vocational University (TVU), Tehran, Iran.
    2. Department of Electrical Engineering, Technical and Vocational University (TVU), Tehran, Iran.
    3. Department of Electrical Engineering, Technical and Vocational University (TVU), Tehran, Iran.


  • Introduction: Immunotherapy, especially personalized vaccines based on neoantigens, has become one of the most promising new approaches in cancer treatment in recent years. These vaccines are designed to specifically stimulate the body's immune system against tumor cells. Neoantigens are specific peptides that are produced as a result of unique genetic mutations in cancer cells and are not present in normal cells of the body. This feature makes them very suitable targets for the immune system, especially in the field of tumor immunotherapy. The presentation of neoantigens by MHC molecules on the surface of tumor cells facilitates their recognition by T cells. In this regard, the accurate recognition of these presented peptides is of vital importance, because incorrect or incomplete selection of neoantigens may reduce the effectiveness of the vaccine or even cause unwanted immune reactions. In this regard, mass spectrometry, as a highly accurate tool, provides the ability to directly identify peptides associated with MHC molecules and is effectively used in the design of personalized cancer vaccines. Unlike purely genomic analyses that are based on theoretical predictions, this method allows for the actual identification of peptides present on the surface of cells. A detailed understanding of mass spectrometry methods and recognition of its capabilities in the field of immunopeptidomics can play a decisive role in the development of new cancer treatments. This article reviewed the principles, implementation steps, tools and challenges associated with the application of this method in the identification of neoantigens and the development of specific vaccines.
  • Methods: The present study is review-based analytical research and is based on a review of authoritative scientific documents, research articles published in international databases such as PubMed, Scopus, and Web of Science, as well as reports published by institutions such as the World Health Organization (WHO) and the US National Cancer Institute (NCI). The focus of this study is on a comprehensive examination of the performance of mass spectrometry devices and their role in the direct identification of neoantigens from the surface of cancer cells. Data analysis was based on experimental reports, clinical studies, and technologies used in important projects such as NeoVa , BNT122, and the Human Immunopeptidome Project. The research method included the following steps: • Collection of structural data on the principles of mass spectrometry (MS) and its sub-fields such as LC-MS/MS, Orbitrap, and TOF. • Exploring the biological mechanisms of antigen processing and presentation by MHC class I molecules. • Step-by-step analysis of sample preparation, ionization, ion separation, detection, and bioinformatics analysis. • Comparison of successful case studies in the design of personalized vaccines using MS-extracted neoantigens.
  • Results: The findings from recent studies show that mass spectrometry is one of the most accurate and reliable methods for the direct detection of neoantigens on the surface of MHC molecules. Modern instruments such as the Orbitrap Exploris™ 480 and the Bruker timsTOF Pro are capable of detecting peptides at very low concentrations and have shown more effective performance than methods based solely on genomic prediction. Research conducted at leading institutions such as the Dana-Farber Cancer Institute, BioNTech, and the Wellcome Sanger Institute has demonstrated that the combination of genomic, transcriptomic, and mass spectrometry data significantly increases the effectiveness of immunotherapy vaccine design. The use of LC-MS/MS in personalized therapy projects has also led to increased patient immune response rates, reduced unwanted side effects, and improved therapeutic efficacy.
  • Conclusion: With the rapid development of bioanalytical technologies, especially in the fields of immunology and oncology, mass spectrometry has become a key component of personalized vaccine design. Its ability to identify peptides actually presented by MHCs is its main advantage over genomic prediction-based methods. Although there are challenges such as high cost, the need for advanced infrastructure, and complex bioinformatics analyses in the development process, its numerous advantages such as high accuracy, reduced risk of unwanted immune responses, and the ability to adapt to the genetic conditions of the patient make this method an irreplaceable tool in future-oriented medicine. With continued advances in machine learning, peptide databases, and single-cell technologies, mass spectrometry is expected to become an integral part of cancer therapeutic approaches in the coming decades.
  • Keywords: Neoantigen, Personalized cancer vaccine, Mass spectrometry, Tumor-specific antigens, Immunotherapy