Projects
Final Report
My final project for CELL 6351 - Intro to Reproducible Data Analysis Using R
Our lab has obtained plasma samples from patients who were infected with COVID-19 between the months of May and November 2020. We ran the plasma over an immunoaffinity purification column with a pan-class I antibody to extract soluble HLA (sHLA), and we eluted the sHLA in acid to denature the MHC molecules and obtain peptides presented by class I sHLA. The eluate was then run through high-performance liquid chromatography (HPLC) to fractionate based on hydrophobicity and separate peptides from full proteins. Next, the peptide fractions were run on a time-of-flight (TOF) mass spectrometer to identify peptide sequences and their associated proteins and genes with high-resolution mass accuracy. I plan on doing our typical data cleanup pipeline in R, showing the distribution of peptide lengths, source proteins, and genes to see if we can identify any COVID-19 peptides. Next, I will perform a more thorough mining of the data by 1) Identifying the peptides with the largest overall intensity across all fractions and 2) individual peptides with the highest intensity peaks. I will then perform a GO Term analysis, KEGG pathway analysis and Reactome analysis on all peptides and show the top 15 results.