MassIVE MSV000080877

Complete Public PXD006230

Proteomics and Phosphoproteomics of an Inducible HIV

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Description

The mechanisms by which human immunodeficiency virus (HIV) circumvents cellular defense machinery to replicate and persist in cells are not fully understood. HIV accessory proteins play key roles in the HIV life cycle by altering host signaling pathways that are highly dependent on post-translational modification (PTM) events. Thus, the identification of HIV accessory protein host targets and their PTM status is critical to fully understand how HIV invades, avoids detection and replicates to spread infection. To date, a comprehensive characterization of HIV accessory protein host targets and modulation of their PTM status does not exist. The significant gap in knowledge regarding the identity and PTMs of HIV host targets is due, in part, to technological limitations. Through this study we sought to apply current mass spectrometry techniques to define mechanisms of viral protein action through identifying host protein interaction partners of Vpr and modulation of down-stream PTM based signaling pathways. Here we report identification and abundance dynamics of over 7,000 proteins and 28,000 phospho-peptides. By utilizing a novel, inducible HIV-1 CD4+ T-cell model system, we overcame challenges associated with synchronization and infection present in other models. This inducible HIV-1 model, in conjunction with state of the art quantitative multiplexed proteomics, allowed for accurate assessment of early protein and PTM dynamics associated with induction of HIV expression. This thorough characterization of Vpr interactions and PTM temporal dynamics, assessed by comparing the wild type with a Vpr deficient strain, deepens the understanding of how HIV circumvents immunity to hijack host cells. This study acts as a resource that lays the foundation for validating host proteins and important PTM based signaling pathways as viable intervention targets. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: HIV ; Jurkat ; TMT ; Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		David Gonzalez, UCSD, United States
Submitting User: jlapek

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Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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