Data-independent mass spectrometry strategies for the identification of atRA-mediated protein signatures of differential cellular response

Abstract

Mass spectrometry is a powerful proteomics tool. Advancements in instrumentation and data acquisition techniques allow researchers to identify and quantify thousands of proteins from cellular samples in a high throughput fashion. Here, I examine the field of data-independent acquisition strategies. More specifically, I illustrate the development of a novel CSI PAcIFIC approach to reduce the total sample analysis time from 4.2 days to 12 hours without deleteriously affecting the quality and quantity of protein identifications. This CSI PAcIFIC method is then used to expand the understanding of the divergent cellular response of MCF-7 and HepG2 cells when treated with all-trans retinoic acid. In this dissertation, I also propose a new technique for identifying poly-ADP-ribosylation via CID mass spectrometry. Enzymatic simplification of the heterogeneous post-translational modification proves valuable for the efficient identification of covalently modified amino acids.