PXD013766-1

PXD013766 is an original dataset announced via ProteomeXchange.

Title	Top Down Histone H4 - SUM159 Butyrate
Description	Proteins physiologically exist and function as ‘proteoforms’ that arise from one gene but acquire additional function by further variation such as post-translational modification (PTM). When multiple PTMs coexist on single protein molecules top down proteomics becomes the only feasible method; however, most top down methods have limited quantitative capacity and insufficient throughput to truly address proteoform biology. Here we demonstrate that, with meticulous design and diligent consideration of statistics, top down proteomics is 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, including gene expression. 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 online C-3 chromatography, narrowly isolated in MS1 and sequenced with ETD fragmentation. With this method we achieve more than 30 replicates from a single 35mm tissue culture dish by loading 55ng of H4 on column. Parallelization and automation yield a sustained throughput of 12 replicates per day, operating continuously for weeks. 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:30:17.612.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew Holt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; phosphorylated residue; acetylated residue; dimethylated residue; N6,N6,N6-trimethyl-L-lysine
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-08 04:24:41	ID requested
⏵ 1	2024-10-07 13:30:18	announced

Holt MV, Wang T, Young NL, High-Throughput Quantitative Top-Down Proteomics: Histone H4. J Am Soc Mass Spectrom, 30(12):2548-2560(2019) [pubmed]

10.1007/s13361-019-02350-z;

submitter keyword: Top-Down, Histone H4

Nicolas L. Young
contact affiliation	Biochemistry, Baylor College of Medicine
contact email	nlyoung@bcm.edu
lab head
Matthew Holt
contact affiliation	BCM
contact email	mvholt@bcm.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD013766
     1. Label: PRIDE project
     2. Name: Top Down Histone H4 - SUM159 Butyrate