JoVE | Peer Reviewed Scientific Video Journal

TOPICAL COLLECTIONS

Cutting-edge Technologies Driving Quantitative Mass Spectrometry

Guest Editors

Nathan Avaritt

University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology

Dr. Nathan Avaritt is an Instructor in the Department of Biochemistry and Molecular Biology at the University of Arkansas for Medical Sciences, where he also completed his Ph.D. in 2014 with a focus on the epigenetic regulation of melanoma progression and on developing methods to effectively utilize fixed tissue samples for proteomics analysis. From 2014 to 2016, Dr. Avaritt worked in the environmental compliance field but was recruited back to UAMS in early 2016 to establish the Developmental Proteomics Laboratory in partnership with Dr. Alan Tackett at the Arkansas Children’s Research Institute (ACRI). In this capacity, Dr. Avaritt facilitated collaborative and translational research projects for dozens of clinicians and scientists, developed the first-in-the-state single cell sequencing pipeline, and also maintained his own research efforts in the field of melanoma epigenetics. In 2020, Dr. Avaritt transitioned from ACRI to the Winthrop P. Rockefeller Cancer Institute to guide and manage a National Cancer Institute research program investigating novel melanoma therapeutics.

Stephanie Byrum

University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology; IDeA National Resource for Quantitative Proteomics, Director of Bioinformatics

Dr. Stephanie Byrum is an Assistant Professor in the Department of Biochemistry and Molecular Biology at the University of Arkansas for Medical Sciences. Dr. Byrum is also the Director of Bioinformatics for the IDeA National Resource for Quantitative Proteomics. She received her PhD in Bioinformatics via the joint UAMS/UALR Bioinformatics program in Little Rock, AR in 2009 with a focus on proteomics analysis. Dr. Byrum conducted her postdoctoral research in the laboratory of Dr. Alan Tackett, where she developed the ChAP-MS technology, which provided the first-ever method to purify a single genomic locus for proteomic identification of bound proteins and histone post-translational modifications. Her current research interests include developing bioinformatics workflows for quantitative proteomics, proteogenomics, meta-proteomics, and multi-omics data integration.

Collection Overview

Proteomics approaches can include detection and quantification of the proteins present and the specific post-translational modifications (PTMs) at a certain cellular state, as well as the proteins coming together in specific organelles or macromolecular protein complexes in certain stoichiometries. Proteomics is a diverse field that can be partitioned into general and quantitative workflows. Quantitative proteomics is focused on determining the amount of protein or protein PTM in a sample and can be classified into targeted-validation and discovery phases. Discovery-phase proteomics generally is known to utilize 10s of samples and generate 1000s of candidate proteins for follow-up studies. Targeted proteomics generally is known to utilize 100s of samples to measure 10s of target proteins. Discovery and targeted proteomics use different types of mass spectrometer configurations, sample preparation methods, and data analysis strategies. The goal of this Methods Collection is to assemble cutting-edge methods that improve proteomics capabilities to sequence deeper into the proteome with less starting material, perform quantitative proteomics with difficult tissue types, improves overall quantitation of proteins and PTMs, and aid in the visualization of proteomics data through bioinformatics workflows.