PXD029956

PXD029956 is an original dataset announced via ProteomeXchange.

Title	Comparative Analysis of T Cell Spatial Proteomics and the Influence of HIV Expression
Description	As systems biology approaches to virology have become more tractable, it has become possible to analyze highly studied viruses such as HIV in new, unbiased ways, including spatial proteomics. We have employed here a differential centrifugation protocol to fractionate an inducible model of HIV-expression in Jurkat T cells for proteomic analysis by mass spectrometry. Using these proteomics data, we evaluated the merits of several reported machine learning pipelines for classification of the spatial proteome and identification of protein translocations. From these analyses we found that classifier performance was organelle-dependent, with Bayesian t-augmented Gaussian mixture modeling outperforming support vector machine (SVM) learning for mitochondrial and ER proteins, but underperforming on cytosolic, nuclear, and plasma membrane proteins by QSep analysis. We also observed a generally higher performance for protein translocation identification using a Bayesian model, BANDLE, on SVM-classified data. Comparative BANDLE analysis of WT and ΔNef models also identified known Nef-dependent interactors such as TCR signaling and coatomer complex. Lastly, we found that SVM classification showed higher consistency and was less sensitive to HIV-dependent noise in our data. These findings illustrate important considerations for future studies of the spatial proteome following viral infection or expression where their generalizability can be further assessed.
HostingRepository	PRIDE
AnnounceDate	2022-01-16
AnnouncementXML	Submission_2022-01-16_14:35:37.707.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alicia Richards
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-26 03:51:12	ID requested
1	2022-01-16 14:27:16	announced
⏵ 2	2022-01-16 14:35:38	announced	2022-01-16: Updated publication reference for PubMed record(s): 35017099.

Oom AL, Stoneham CA, Lewinski MK, Richards A, Wozniak JM, Shams-Ud-Doha K, Gonzalez DJ, Krogan NJ, Guatelli J, Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression. Mol Cell Proteomics, 21(3):100194(2022) [pubmed]

submitter keyword: Spatial proteomics, HIV-1, LC-MS/MS

Dr. Nevan Krogan
contact affiliation	Department of Cellular and Molecular Pharmacology
contact email	nevan.krogan@ucsf.edu
lab head
Alicia Richards
contact affiliation	Krogan lab
contact email	alicia.richards@ucsf.edu
dataset submitter

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/pride/data/archive/2022/01/PXD029956

PRIDE project URI

• PRIDE
  1. PXD029956
     1. Label: PRIDE project
     2. Name: Comparative Analysis of T Cell Spatial Proteomics and the Influence of HIV Expression