Audrey Kishishita

PhD Chemical Biologist specializing in advanced proteomics and mass spectrometry with 6+ years of research experience. My current research focuses on identifying tumor-specific protein conformations at the cell surface across various hematological malignancies using novel structural proteomics approaches (patent pending). I've developed expertise in crosslinking mass spectrometry (XL-MS), having co-invented a patented platform for cell surface structural proteomics. My technical skills span protein purification, LC-MS/MS operation and method development (Orbitrap Eclipse, timsTOF Pro), and computational analysis of complex proteomics datasets.

Beyond XL-MS, I'm proficient in diverse quantitative proteomics workflows (SILAC, TMT, LFQ), in vitro protein expression and purification, and cellular engineering. I've contributed to open-source structural proteomics software and regularly present my research at national conferences including ASMS. I thrive in collaborative environments and am passionate about applying proteomics, mass spectrometry, and protein biochemistry techniques to advance therapeutic discovery and development.

PhD candidate in Chemical Biology (UCSF, expected Aug 2025) with expertise in proteomics, mass spectrometry, protein biochemistry, and AI-guided protein modeling. Skilled in HPLC and LC-MS method development (patent #PCT/US2025/0243023) as well as data analysis. Applied TensorFlow, ESM1b, and AlphaFold to integrate structure prediction with experimental small molecule and PTM data. Experience with characterizing novel small molecule and crosslinker adducts upon treatment in cell line models using AP-MS and PRM. Proven collaborator and communicator with publications, mentoring experience, and national presentations.

SELECTED HIGHLIGHTS

Patent: LC-MS proteomics with fractionation platform for enhanced protein structure mapping 
Software Contribution: UI & co-dev, AlphaCross-XL (open-source structural proteomics tool)
Mentorship: Trained 3+ rotating PhD students and maintained lab documentation protocols

TECHNICAL SKILLS

Proteomics & Biochemistry: quantitative, structural, and cell surface proteomics; affinity capture-MS; multidimensional peptide fractionation; western blot; flow cytometry; protein/antibody purification; transgenic cell line generation
Instrumentation: LC-MS (Orbitrap Eclipse, timsTOF Pro 2), HPLC (SEC, RP, CEX, affinity), confocal & SEM microscopy, FACS, spectroscopy
Computational & Modeling: Python, R, C++, bash scripting, TensorFlow, AlphaFold, ESM1b, molecular dynamics, biomolecular docking, HPC clusters

PhD, Chemical Biology — University of California, San Francisco, Expected Aug 2025
MS, Chemistry — California State University, Los Angeles, 2019
BS, Microbiology — California State University, Los Angeles, 2017