We propose to develop, validate, and apply a suite of powerful new tools to interrogate the functions, interactions, and cellular localizations of individual splice variants of HIV-1, which is the virus that causes AIDS and infects over 1 million people each year.
 

Given the importance of the mutants of KRAS, and related Ras genes, as driving oncogenes in such a large percentage of tumors, we will use mass spectrometry to evaluate in vitro cleavage of peptides mutated in KRAS by cathepsin B.
 

We propose to investigate the importance and origin of a fascinating modification that we recently discovered to the HIV structural proteins, namely the formation of dehydroamino acids.  HIV is the virus that causes AIDS and infects over 1 million people each year.  We will examine the role of these modification in the HIV life cycle and evaluate their purpose.
 

UW-Madison will be responsible for the creation of software to effectively identify and quantify peptides in this project. During the initial phase of the research project, the MetaMorpheus software program, originally created by our group, will be updated to enable improved match between runs quantification of the peptides in single cell proteomics experiments.
 

The goal is to create a dedicated software module within MetaMorpheus for the identification of peptides in single-cell proteomics (SCP) data.
 

The proposed research aims to elucidate the biological functions of lncRNAs and their associated proteins to discover GATA factor-dependent regulatory circuits and networks that control hematopoiesis.

The proposed research aims to identify lncRNA-protein complexes that correlate with tumor aggressiveness in human prostate cancer samples and quantify the constituent lncRNAs and associated proteins.

This project applies high-resolution imaging, RNA-capture proteomics, and cell-based assays to elucidate new features of HIV-1 RNA nuclear export and genome trafficking in the cytoplasm, with the long-term goal of informing the development of anti-HIV-1 therapeutic strategies that block these stages.
 

The focus of this grant is the development of novel technologies for proteomics and biological mass spectrometry with an emphasis on comprehensive proteoform identification and quantification in complex systems.