PXD000172

PXD000172 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes
Description	Methylation of lysine 4 at histone H3 (H3K4) at promoters is tightly linked to transcriptional regulation in human cells. At least six different COMPASS-like multi-subunit (SET1/MLL) complexes have been described that contain methyltransferase activity towards H3K4, but a comprehensive and quantitative analysis of these SET1/MLL complexes is lacking. We applied label-free quantitative mass spectrometry to determine the subunit composition and stoichiometry of the human SET1/MLL complexes. Peptides were applied to online nanoLC-MS/MS, using a 120 min acetonitrile gradient (5.6 - 76%). Mass spectra were recorded on an LTQ-Orbitrap-Velos mass spectrometer (Thermo) selecting the 15 most intense precursor ions of every full scan for fragmentation. Raw data were analyzed using MaxQuant 1.3.0.5, with label-free quantification (LFQ), match between runs (between triplicates) and the iBAQ algorithm enabled. MaxQuant default settings were used for peptide identification; Enzyme: Trypsin/P, MS tolerance (FTMS): 6 ppm, max missed cleavages: 2, max charge: 7, MS/MS tolerance (ITMS): 0.5 Da, Peptide FDR: 0.01 and Protein FDR: 0.01. Normalized mass spectrometric intensities (LFQ intensities) were compared between the GFP-tagged and control sample, using an adapted permutation-based false discovery rate (FDR) t-test in Perseus (MaxQuant package).
HostingRepository	PRIDE
AnnounceDate	2013-09-13
AnnouncementXML	Submission_2013-09-13_03:46:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	A.H. Smits
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue; monohydroxylated residue; acetylated residue
Instrument	LTQ Orbitrap Velos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2013-03-04 05:37:51	ID requested
1	2013-05-02 03:56:25	announced
1	2014-07-25 00:57:43	announced
2	2013-05-02 04:03:20	announced	Add reference
⏵ 3	2013-09-13 03:46:37	announced	missing

Publication List

van Nuland R, Smits AH, Pallaki P, Jansen PW, Vermeulen M, Timmers HT, Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes. Mol Cell Biol, 33(10):2067-77(2013) [pubmed]

van Nuland R, Smits AH, Pallaki P, Jansen PW, Vermeulen M, Timmers HT, Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes. Mol Cell Biol, 33(10):2067-77(2013) [pubmed]

Keyword List

submitter keyword: human, SET1, MLL, COMPASS, histone methylation, MS

submitter keyword: human, SET1, MLL, COMPASS, histone methylation, MS

Contact List

A.H. Smits
contact affiliation	University Medical Center Utrecht
contact email	a.smits-4@umcutrecht.nl

Full Dataset Link List

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/2013/09/PXD000172

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/2013/09/PXD000172