One of the major work of the teams of analytical chemists at Philip Morris International R&D is to characterize and quantify the chemical composition of the aerosols generated by the new tobacco-heated products. Analytical chemists use various gas chromatographic instruments coupled to mass spectrometry (MS) that are each from different providers linked to different deconvolution and MS processing software. Hence, the team of Computational Chemistry at PMI developed a complex software platform called Computer-Assisted Structure Identification (CASI) that help to automate these processes, integrate them together, enhance the accuracy of the correct compound identification using scientific calculations, and provide instant reporting. Many elements of this platform are developed and successfully implemented using Pipeline Pilot (PP). We will present examples of PP protocols: at which points they are plugged-in to the CASI platform, what protocols are processing structures found in spectral libraries (standardization, boiling point calculation), how the SMART-coded rules help to determine correct internal standards and finally how the results are reported in user-desired formats.