PXD013766 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-05-08 04:24:41 | ID requested | |
⏵ 1 | 2024-10-07 13:30:18 | announced | |
Publication List
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; |
Keyword List
submitter keyword: Top-Down, Histone H4 |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD013766
- Label: PRIDE project
- Name: Top Down Histone H4 - SUM159 Butyrate