Chris Petzold, Ph.D., is is a research scientist with Lawrence Berkeley National Laboratory and Director of Proteomics of the Joint BioEnergy Institute. He obtained his Ph.D. in Chemistry from Purdue University with emphasis in gas-phase ion chemistry and mass spectrometric methods development. After graduating from Purdue, he performed his post-doctoral work at UC-Berkeley focusing on mass spectrometry-based glycomics and lipidomics research. At the Joint BioEnergy Institute the proteomics team develops quantitative methods to aid synthetic biology efforts to engineer microbes for biofuel production. This work furthers rational design and optimization of novel metabolic pathways for many synthetic biology applications.

A Skyline-based workflow for rapid development of high-throughput quantitative proteomic assays

Quantitative proteomic assays are a key component of a wide variety of studies in biotechnology research, especially for synthetic biology and metabolic engineering applications that often involve sample sets in the hundreds or thousands. Read More
Complicating the analysis further is the fact that the target proteins and organisms of interest are often different across experiments. Consequently, we have developed a Skyline-based workflow utilizing spectral libraries generated from shotgun proteomics experiments, iRT-based retention time prediction, and highly reproducible standard flow chromatography that enables the use of narrow retention time windows to minimize concurrent transitions and optimize sensitivity. With this workflow we can directly and reliably translate peptide identification data from 120-minute gradient shotgun proteomic runs to scheduled MRM experiments with 2-minute gradients. We have applied the workflow to quantify proteins in >10 different microbes, including targeting >50 proteins from more than 3000 samples (>500 strains, 2 conditions, 3 replicates) of Escherichia coli.