PXD016843

PXD016843 is an original dataset announced via ProteomeXchange.

Title	Characterization of plasma proteins of HIV/AIDS patients underfirst line anti-retroviral therapy
Description	The retrospective cohort study was focused on the first line ART patients who were enrolled in the antiretroviral therapy center, Sarojini Naidu Medical College, Agra, India from December 2009 to November 2016. The main criteria for inclusion was based on the immunological marker, i.e. CD4+ count (<350). The all age group adults and adolescents were included in this study. The informed consents were obtained from all patients. A patient information leaflet was used for collection of sociodemographic and clinical profile data. This study protocol was approved by Institute human ethics committee. The Institute ethics committee is constituted as per the guidelines directed by Indian Council of MedicalResearch. Ten ml of blood samples were collected from a total of six AIDS patients after counselling whose CD4+ count was <350 cells/µl. Then plasma was separated by centrifugation at 2000g for 10 minutes. Then plasma was stored at -800C for estimation of viral load and genotyping was carried out at NIRT, ICMR, Chennai, Tamilnadu, India.The viral load was estimated using Abbott automated m2000rt instrument. Those who were having>1000 copies/ml called as a drug resistant and < 1000 copies/ml called as drug responder. Among them, 3 patients were having high viral load >1000 copies/ml (drug resistant and 3 patients were with <1000 copies/ml (drug responder). The 3 treatment failure (>1000 copies/ml) samples were further considered for genotype analysis. Highly abundant proteins (Albumin and IgG) were depleted using the Aurum–Serum protein mini kit (Biorad, USA). The depleted plasma samples were analyzed in SWATH-MS. Then, the proteins were identified and characterized using the SWATH analysis.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:06:30.680.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Keshar Kunja Mohanty
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-19 05:57:01	ID requested
1	2023-10-24 07:58:39	announced
⏵ 2	2023-11-14 09:06:31	announced	2023-11-14: Updated project metadata.

Barik SK, Tripathy SP, Bisht D, Singh P, Chakraborty R, Patil SA, Singh TP, Varshney D, Jena S, Mohanty KK, SWATH-MS analysis of plasma proteins among Indian HIV-1 infected patients. Bioinformation, 19(4):392-398(2023) [pubmed]

curator keyword: Biomedical

submitter keyword: HIV, AIDS, SWATH-MS, ART, Human Plasma Proteins

Dr(Mrs) Keshar Kunja Mohanty
contact affiliation	Dr(Mrs) Keshar Kunja Mohanty Scientist F, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Taj Ganj, Agra - 282004, Uttar Pradesh, India
contact email	keshar63@yahoo.com
lab head
Keshar Kunja Mohanty
contact affiliation	ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases
contact email	keshar63@yahoo.com
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/2023/10/PXD016843

PRIDE project URI

• PRIDE
  1. PXD016843
     1. Label: PRIDE project
     2. Name: Characterization of plasma proteins of HIV/AIDS patients underfirst line anti-retroviral therapy