PXD047528

PXD047528 is an original dataset announced via ProteomeXchange.

Title	Using Plasma Proteomics to Investigate Viral Infections of the Central Nervous System including Patients with HIV-Associated Neurocognitive Disorders
Description	State-of-the-art liquid chromatography/mass spectrometry (LC/MS)-based proteomic technologies, using microliter amounts of patient plasma, can detect and quantify several hundred plasma proteins in a high throughput fashion, allowing for the discovery of clinically relevant protein biomarkers and insights into the underlying pathobiological processes. Using such an in-house developed high throughput plasma proteomics allowed us to identify and quantify > 400 plasmas proteins in 15 minutes per samples, i.e., a throughput of 100 samples/day. We demonstrated the clinical applicability of our method in this pilot study by mapping the plasma proteomes from patients infected with human immunodeficiency virus (HIV) or herpes virus, both groups with involvement of the central nervous system (CNS). We found significant disease-specific differences in the plasma proteomes. The most notable difference was a decrease in the levels of several coagulation-associated proteins in HIV vs. herpes virus, amongst other dysregulated biological pathways providing insight into the differential pathophysiology of HIV compared to herpes virus infection. In a subsequent analysis, we found several plasma proteins associated with immunity and metabolism to differentiate patients with HIV-associated neurocognitive disorders (HAND) compared to cognitively normal people with HIV (PWH), suggesting the presence of plasma-based biomarkers to distinguishing HAND from cognitively normal PWH. Overall, our high-throughput plasma proteomics pipeline enables identification of distinct proteomic signatures of HIV and herpes virus, which may help illuminate divergent pathophysiology behind virus-associated neurological disorders.
HostingRepository	PRIDE
AnnounceDate	2024-03-05
AnnouncementXML	Submission_2024-03-05_10:21:07.902.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Saima Ahmed
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-05 03:21:36	ID requested
⏵ 1	2024-03-05 10:21:08	announced

10.1007/S13365-022-01077-0;

submitter keyword: plasma proteomics DIA

Hanno Steen
contact affiliation	Harvard Medical School , Boston Children's Hospital
contact email	saima.ahmed@childrens.harvard.edu
lab head
Saima Ahmed
contact affiliation	Boston Children's Hospital
contact email	saima.ahmed@childrens.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD047528
     1. Label: PRIDE project
     2. Name: Using Plasma Proteomics to Investigate Viral Infections of the Central Nervous System including Patients with HIV-Associated Neurocognitive Disorders