High-Throughput Quantitative Top-Down Proteomics: Histone H4
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J. Am. Soc. Mass Spectrom. (2019) DOI: 10.1007/s13361-019-02350-z
FOCUS: 34 t h ASILOMAR CONFERENCE, QUANTITATIVE ANALYSIS OF PTMS: s RESEARCH ARTICLE
High-Throughput Quantitative Top-Down Proteomics: Histone H4 Matthew V. Holt,1 Tao Wang,1 Nicolas L. Young1,2 1
Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, USA Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
2
Abstract. Proteins physiologically exist as “proteoforms” that arise from one gene and acquire additional function by post-translational modifications (PTM). When multiple PTMs coexist on single protein molecules, top-down proteomics becomes the only feasible method of characterization; however, most top-down methods have limited quantitative capacity and insufficient throughput to truly address proteoform biology. Here we demonstrate that top-down proteomics can be quantitative, reproducible, sensitive, and high throughput. The proteoforms of histone H4 are well studied both as a challenging proteoform identification problem and due to their essential role in the regulation of all eukaryotic DNA-templated processes. Much of histone H4’s function is obfuscated from prevailing methods due to combinatorial mechanisms. Starting from cells or tissues, after an optimized protein purification process, the H4 proteoforms are physically separated by on-line C3 chromatography, narrowly isolated in MS1 and sequenced with ETD fragmentation. We achieve more than 30 replicates from a single 35-mm tissue culture dish by loading 55 ng of H4 on column. Parallelization and automation yield a sustained throughput of 12 replicates per day. We achieve reproducible quantitation (average biological Pearson correlations of 0.89) of hundreds of proteoforms (about 200–300) over almost six orders of magnitude and an estimated LLoQ of 0.001% abundance. We demonstrate the capacity of the method to precisely measure well-established changes with sodium butyrate treatment of SUM159 cells. We show that the data produced by a quantitative top-down method can be amenable to parametric statistical comparisons and is capable of delineating relevant biological changes at the full proteoform level. Keywords: Histone post-translational modifications, Histone proteoforms, Dynamics of histone modifications, Epigenetic inhibitor, Top-down proteomics Received: 10 May 2019/Revised: 3 October 2019/Accepted: 5 October 2019
Introduction
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op-down proteomics is capable of capturing full proteoform information; however, previous approaches have mostly been non-quantitative, semi-quantitative, or have suffered from moderate to poor reproducibility. High sample
Electronic supplementary material The online version of this article (https:// doi.org/10.1007/s13361-019-02350-z) contains supplementary material, which is available to authorized users. Correspondence to: Nicolas Young; e-mail: [email protected]
requirements and low throughput have mostly limited the scope of top-down proteomics t
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