PXD000208

PXD000208 is an original dataset announced via ProteomeXchange.

Title	AP-MS analysis of human histone deacetylase interactions in CEM-T cells
Description	Affinity purification-mass spectrometry (AP-MS) datasets of eleven human histone deacetylases (HDACs). Affinity-tagged (GFP) HDACs were expressed in a human CEM-T cell line. For label-free analysis, proteins were digested by trypsin in-solution and peptides separated across a linear 180 min gradient by a one-dimensional LC-MS/MS analysis. For label-free analysis, MS data (RAW files) were converted into mzXML format using the Proteowizard conversion tool. mzXML files were searched using the X!Tandem/k-score database search tool against the human subset of the UniProt protein sequence database, appended with a list of common sample contaminants. The search results were processed using PeptideProphet and ProteinProphet tools. The data from individual experiments across 7 biological replicates of GFP controls and 23 HDAC-GFP-tagged biological replicates were merged, and the spectral counts were extracted using the software, ABACUS. The combined list of protein identifications (protein groups) was filtered to achieve a protein-level FDR of less than 1%. When computing the spectral counts in individual experiments, proteins were quantified (i.e. spectra counted) if they were identified with a probability equal or greater than 0.9 in that particular replicate. For metabolic labeling IDIRT experiments, isolated proteins were separated by SDS-PAGE, digested by trypsin in-gel, and peptides were separated across a linear 90 min gradient. RAW files were processed and peptides were identified (less than 1% FDR) and quantified using SEQUEST/Percolator in the Proteome Discoverer software (v1.3). IDIRT protein ratios were normalized by the median SILAC protein ratio determined from 1D-LC-MS/MS analysis of input lysates. Protein interactions have been submitted to the IMEx consortium through IntAct with the identifier IM-18733.
HostingRepository	PRIDE
AnnounceDate	2013-06-14
AnnouncementXML	Submission_2013-06-14_02:22:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	T Greco
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue; monohydroxylated residue; (R)-5-oxo-1: 4-tetrahydrothiazine-3-carboxylic acid; 2-pyrrolidone-5-carboxylic acid (Glu); 2-pyrrolidone-5-carboxylic acid (Gln); 6x(13)C: 2x(15)N labeled L-lysine; 6x(13)C labeled L-arginine; deaminated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-04-09 06:55:28	ID requested
1	2013-06-14 02:18:19	announced
1	2014-07-25 01:03:53	announced
⏵ 2	2013-06-14 02:22:32	announced	Add reference

Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM, The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol, 9():672(2013) [pubmed]

submitter keyword: HDAC, AP-MS, protein interactions, IDIRT

T Greco
contact affiliation	Princeton University
contact email	tgreco@princeton.edu

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