Shotgun mass spectrometry-based proteomics has emerged as the most powerful approach to comprehensively analyze proteins in a biological sample over the last few years. This technology will play a key role in the predictive, preventive, personalized, and participatory medicine design. Correct peptide identification from a tandem mass spectrum is the crucial step to determine the target protein sequence and it is indeed one of the most challenging topics in Bioinformatics. Nowadays, the instrument venders have successively refined their mass analyzers to generate different types of tandem mass spectra simultaneously. We proposed a novel research to utilize the useful information brought by this new technology. The collaboration with Bioinformatics Solutions Inc. allows my research outcome to be rapidly applied to, and tested by real-life applications, as the company plans to incorporate the research outcome in their successful commercial product.