Josue Baeza Josue Baeza is a postdoctoral fellow in the laboratory of Dr. Benjamin Garcia at the University of Pennsylvania. He obtained his Ph.D. at the University of Wisconsin-Madison under the mentorship of Dr. John Denu. During his Ph.D., he developed a chemical labeling strategy to quantify lysine acetylation stoichiometry and applied this method to determine rates of non-enzymatic acetylation (measured as second-order rate constants) as well as histone acetylation turnover rates. As a postdoctoral fellow in the Garcia Lab, Josue is interested in understanding mechanisms regulating protein turnover including how changes in protein turnover influence the epigenetic landscape as well as developing methods to quantify protein turnover in vivo.

Applications of Skyline for Method Development and Quantification of Histone Marks

Despite a growing interest in epigenetics, performing proteomics studies of histone tail marks remains highly specialized. Mass spectrometry of histone tail marks is difficult due to the variety of modifications, coeluting isoforms, and dynamic range. Conventionally, these challenges have been met with database searching shotgun DDA, which detects histone marks but doesn’t provide accurate quantification; or optimizing high-level PRM methods, which accurately quantifies but cannot detect novel histone marks. Here, we have designed a robust histone DIA method and a flexible Skyline-based analysis workflow to more accurately and precisely quantify histone marks. Read More
Our DIA-MS Skyline-based workflow for quantifying histone tail modifications takes advantage of Skyline’s latest features, including staggered DIA isolation window demultiplexing to process raw data, the “Quantitative” fragment ion demarcation for site-localizing isobaric histone marks, and a retention time calculator that uses co-enriched peptides as iRT anchors. Our workflow and an accompanying tutorial are available on Panorama Public.