An open-source computational and data resource to analyze digital maps of immunopeptidomes
Caron E., Espona L., Kowalewski DJ., Schuster H., Ternette N., Alpízar A., Schittenhelm RB., Ramarathinam SH., Lindestam Arlehamn CS., Chiek Koh C., Gillet LC., Rabsteyn A., Navarro P., Kim S., Lam H., Sturm T., Marcilla M., Sette A., Campbell DS., Deutsch EW., Moritz RL., Purcell AW., Rammensee H-G., Stevanovic S., Aebersold R.
We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.