PXD000064

PXD000064 is an original dataset announced via ProteomeXchange.

Title	The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types
Description	HIV-1 incorporates a large array of host proteins into virions. Determining the host protein composition in HIV virions has technical difficulties, including co-purification of microvesicles. We developed an alternative purification technique using cholesterol that differentially modulates the density of virions and microvesicles (density modification, DM) allowing for high-yield virion purification that is essential for tandem mass spectrometric and quantitative proteomic (iTRAQ) analysis. DM purified virions were analyzed using iTRAQ and validated against Optiprep (60% iodixanol) purified virions. We were able to characterize host protein incorporation in DM-purified HIV particles derived from CD4+ T cell lines; we compared this dataset to a reprocessed dataset of monocyte-derived macrophages (MDM) derived HIV-1 searched using PrpArML which uses multiple search algorithms (OMSSA, X!Tandem with native, k-score and s-score scoring, MASCOT, MyriMatch, and InSpecT ). The database used for search was the UniProt-SwissProt database (version 2010.11.02; 522,019 sequences). Peptides were combined on PepARML using a random forest approach (Weka) and the results were then parsed into MASPECTRAS 2 with minimum two peptide for a protein and a spectrum false discovery rate of 5%. Peptides assigned  to keratin were excluded, and since the analysis was focused on host proteins, viral peptide assignments were excluded. Protein redundancy was removed by MS based evidence clustering. Link to the paper related to the reprocessed MDM dataset: PMID: 16940516, the dataset itself is not publicly available.
HostingRepository	PRIDE
AnnounceDate	2013-08-02
AnnouncementXML	Submission_2013-08-02_05:43:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ceereena Ubaida Mohien
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Human immunodeficiency virus 1; NCBI TaxID: 11676;
ModificationList	iTRAQ4plex-116 reporter+balance reagent acylated residue; methylthiolated residue; iodoacetamide derivatized residue; monohydroxylated residue
Instrument	LCQ Classic; Applied Biosystems instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2012-11-05 03:55:46	ID requested
1	2013-08-02 05:41:23	announced
1	2014-07-25 00:43:41	announced
⏵ 2	2013-08-02 05:43:34	announced	Add reference

Linde ME, Colquhoun DR, Ubaida Mohien C, Kole T, Aquino V, Cotter R, Edwards N, Hildreth JE, Graham DR, The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types. J Proteome Res, 12(5):2045-54(2013) [pubmed]

submitter keyword: HIV-1, Virions, DM, LC-MS/MS, MDM

Ceereena Ubaida Mohien
contact affiliation	Johns Hopkins School of Medicine
contact email	ceereena@jhmi.edu

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