Dataset Information

The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types

ABSTRACT: 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.

INSTRUMENT(S): LCQ Classic, Applied Biosystems instrument model

ORGANISM(S): Homo Sapiens (human) Human Immunodeficiency Virus 1

SUBMITTER: Ceereena Ubaida Mohien

PROVIDER: PXD000064 | Pride | 2013-08-02

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	DMPurified.zip	Other
	UltraPure_HIV.peparml.pep.xml	Pepxml
	uniprot_sprot.2010_11_20101102.fasta	Fasta

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Publications

The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types.

Linde Michael E ME Colquhoun David R DR Ubaida Mohien Ceereena C Kole Thomas T Aquino Veronica V Cotter Robert R Edwards Nathan N Hildreth James E K JE Graham David R DR

Journal of proteome research 20130329 5

HIV-1 incorporates a large array of host proteins into virions. Determining the host protein composition in HIV virions has technical difficulties, including copurification 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 pu ...[more]

PMID: 23432411

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