Although Next Generation DNA Sequencing can identify tens of thousands of mutations in a cancer genome, the sequencing data alone still cannot accurately predict the T-cell epitopes on the cancer cell surface even with the best neoantigen prediction software. A tremendous amount of work is needed to identify a small number of “true” neoantigens (possibly a few to several dozen) from a large number of candidate peptide sequences.

ProtTech has developed a platform to identify neoantigens by sequencing MHC I and/or MHC II bound peptides by biochemical isolation, e,g, the immunoprecipitation of human MHC I-peptide complex by W6/32 antibodies. The isolated peptides are analyzed by an ultra-sensitive NanoLC-MS/MS. This platform, known as NeoMS, is a proprietary software suite dedicated to the sequencing and analysis of MHC class I and class II antigens, particularly neoantigens presented by tumor cells and antigen-presenting cells (APC). The functionality of the software suite includes:
1). Identifying tumor neoantigens derived from somatic mutations, such as amino acid substitutions, deletion, insertion, reading frame shift in translation, etc;
2). Identifying tumor neoantigens arrived from abnormal expression of the germ cell specific proteins (cancer testis antigens);
3). Identifying intron retention neoantigens.

The software suite has three basic modes of the calculations:
MODE 1: De novo sequencing (no sequence database is required);
MODE 2. Cancer Whole Exon Sequencing database dependent search (an individual cancer whole exon sequencing data is required);
MODE 3. RNAseq dependent search (an individual cancer mRNA NGS data are required. This mode is used for the discovery of the intron retention neoantigens).

The human genome contains 233,785 exons, with the size of human introns being almost 30 times larger than the size of exons. Since up to six reading frames may need to be searched, the required computation power is tremendous. To meet this requirement, we developed our NeoMS software suite based on a parallel computing architect that contains a large number of networked computers carrying out the calculations simultaneously. Please contact us for the analysis of NeoAntigen peptide.