PXD023291

PXD023291 is an original dataset announced via ProteomeXchange.

Title	SWATH-MS and MRM: Quantification of Ras-related proteins in HIV-1 Infected and Methamphetamine-Exposed Human Monocyte-Derived Macrophages (hMDM)
Description	Macrophages are involved in the immunological response to inflammatory and infectious agents, including Human Immunodeficiency Virus type 1 (HIV-1) infection. They are a primary targets of the virus and facilitate transfer across the blood brain barrier into the central nervous system. In the presence of toxic substances, such as methamphetamine (Meth), the protective functions of macrophages are further impaired. It has been shown that both HIV-1 infection and Meth induce changes in the proteome of macrophages. Therefore, in the presented study we employed a nano-liquid chromatography (nanoLC)-SWATH mass spectrometry (MS) approach to detect and quantify changes on proteome level that are induced in human monocyte derived macrophages (hMDM) that were exposed to Meth before or after HIV infection. As we focused in this study on actin and a cluster of Ras-related proteins (Rab), we selected the following proteins: actin (UniProt P60709), Ras-related protein Rab-1A (UniProt P62820), Ras-related protein Rab-2A (UniProt P61019), Ras-related protein Rab-4B (UniProt P61018), Ras-related protein Rab-7A (UniProt P51149), Ras-related protein Rab-9A (UniProt P51151), Ras-related protein Rab-11 (UniProt P62491), Ras-related protein Rab-14 (UniProt P61106), Ras-related protein Rab-22A (UniProt Q9UL26), Ras-related protein Rab-24 (UniProt Q969Q5), Ras-related protein Rab-37 (UniProt Q96AX2) for further validation, which we performed using liquid chromatography-multiple reaction monitoring (LC-MRM) MS technique. The MRM data from this study, along with LC-MRM analysis and data processing parameters, were separately described and deposited in PASSEL repository with accession number PASS01591.
HostingRepository	PRIDE
AnnounceDate	2022-05-19
AnnouncementXML	Submission_2022-05-19_13:55:42.467.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Katarzyna Macur
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-23 05:13:40	ID requested
⏵ 1	2022-05-19 13:55:43	announced

Grabowska K, Macur K, Zieschang S, Zaman L, Haverland N, Schissel A, Morsey B, Fox HS, Ciborowski P, HIV-1 and methamphetamine alter galectins -1, -3, and -9 in human monocyte-derived macrophages. J Neurovirol, 28(1):99-112(2022) [pubmed]

submitter keyword: HIV, macrophages, Ras-related proteis (Rab), actin, methamphetamine, SWATH

Prof. Pawel Ciborowski
contact affiliation	Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985800 University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
contact email	pciborowski@unmc.edu
lab head
Katarzyna Macur
contact affiliation	University of Nebraska Medical Center
contact email	kasia.macur@unmc.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/2022/05/PXD023291

PRIDE project URI

• PRIDE
  1. PXD023291
     1. Label: PRIDE project
     2. Name: SWATH-MS and MRM: Quantification of Ras-related proteins in HIV-1 Infected and Methamphetamine-Exposed Human Monocyte-Derived Macrophages (hMDM)