Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling

Defining the repertoire of peptides presented by the major histocompatibility complex class I (MHC I) is a key step towards the identification of relevant antigens for cancer immunotherapy. However, the identification of the cancer-specific antigens is a significant analytical challenge in view of their low abundance and low mutational load found in primary cancer specimens. Here, we describe the application of isobaric peptide labeling with tandem mass tag (TMT) to improve the detection of the MHC I peptides. Isobaric peptide labeling was found to promote the formation of multiply-charged ions and to enhance the formation of b-type fragment ions, thus resulting in a 50% improvement of MHC I peptide identification. The gain in sensitivity obtained using TMT labeling enabled the detection of low abundance MHC I peptides including tumor-specific antigens (TSAs) and minor histocompatibility antigens (MiHAs). We further demonstrate the application of this approach to quantify MiHAs presented by B-cell lymphocytes and determined their expression levels by LC-MS/MS using both synchronous precursor selection (SPS) and high field asymmetric waveform ion mobility spectrometry (FAIMS).