UROP Proceedings 2020-21

School of Engineering Department of Chemical and Biological Engineering 84 Improving Data Analysis Methods in Proteomics Supervisor: LAM Henry Hei Ning / CBE Student: LEE Jooran / BIEN Course: UROP1100, Spring Peptides from digested proteins are chromatographically separated and fragmented in the mass spectrometer, generating fragment ion spectra that can be used to deduce the corresponding peptide sequences. These Peptide Spectra Matches (PSMs) in turn allow the identification of the proteins in the biological sample. The PSMs, however, are not always correct. Using several well-known machine learning algorithms to separate correct PSMs from the incorrect PSMs was the main purpose of the project. It was done by comparing their accuracy, performance, and time taken for the classification. In addition to that, the feature importance is calculated from each machine learning algorithm and the common important features were extracted that can potentially be used to build a more efficient model for data analysis on proteomics. Second part of this research was based literature review on evaluating computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. Improving Data Analysis Methods in Proteomics Supervisor: LAM Henry Hei Ning / CBE Student: ISLAM Kazi Anisha / CENG Course: UROP1000, Summer The protein modifications of bacteria have not been extensively researched and hence, an investigation of their complexity is worth being carried out. In this project, an open search analysis of E.coli peptide MS2 spectra was conducted. Relatively low numbers of peptide-spectrum matches (PSM) with uncommon modifications (hydroxylation of phenylalanine and tyrosine, di/oxidation of tryptophan, cysteine  dehydroalanine) were identified. Due to the limitations of data dependent acquisition method and a potentially high false negative rate, PSMs of the peptides with the uncommon modifications are observed in low abundance. While oxidation and deoxidation of tryptophan hydroxylation of tyrosine are posttranslational modifications, cysteine  dehydroalanine and hydroxylation of phenylalanine are chemical artifacts. In general, it can be observed that untreated E.coli is less likely to produce proteins with uncommon modifications. Development of Valuable Fine Chemical Products from Wooden Waste by Heterogeneous Catalytic Pyrolysis Supervisor: LAM Leung Yuk Frank / CBE Co-supervisor: HU Xijun / CBE Student: LIEM Albert / SUSEE Course: UROP1100, Fall As a metropolitan and one of the most densely populated places in the world, land prices in Hong Kong is exorbitantly high. With limited land supply and increasing demand for space, comprehensive and strategic planning is required to provide much needed capacity for waste disposal in Hong Kong. With the rapid growth in the logistics and construction sectors, those factors have led to a large demand for wood pallets for easy transportation. Typically, pine pallets are preferred due to its low cost and it cheap enough that pine pallets are often only used once before being abandoned at the end of the supply chain, consequently ending up in landfills and contributing to wood waste that occupies 8-10% of the landfill capacity in Hong Kong. Thus, this project aims to develop specially designed metallic-based catalyst to transform wooden waste to more useful organic compounds such as pyroligneous acid and bio-oil.