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Protocols

PPD specifications

Information


Unique identifier OMICS_03918
Name PPD
Alternative name Plasma Proteome Database
Restrictions to use None
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publications for Plasma Proteome Database

PPD citations

 (5)
library_books

Quantitative proteomic analysis of pancreatic cyst fluid proteins associated with malignancy in intraductal papillary mucinous neoplasms

2018
PMCID: 5907296
PMID: 29713252
DOI: 10.1186/s12014-018-9193-1

[…] Additional file : Table S1). Protein accession numbers were converted into gene names, and the resulting redundancy was discarded prior to comparative analysis. We compared our dataset with the Human Plasma Proteome Database to assess the likelihood that the discovered proteins are potential blood markers [, ]. As a result, 2299 (79.7%) of the identified proteins were plasma proteins (Additional f […]

library_books

Integrative analysis for the discovery of lung cancer serological markers and validation by MRM MS

2017
PLoS One
PMCID: 5570484
PMID: 28837649
DOI: 10.1371/journal.pone.0183896

[…] program (version 2.0, http://www.cbs.dtu.dk/services/TMHMM2.0) was used to predict transmembrane helices in integral membrane proteins []. All of the secreted proteins were further analyzed using the Plasma Proteome Database (PPD, http://www.plasmaproteomedatabase.org). Ingenuity Pathway Analysis (IPA, Ingenuity system, http://www.ingenuity.com) was used to determine the subcellular localizations […]

library_books

Nipple aspirate fluid—A liquid biopsy for diagnosing breast health

2017
Proteomics Clin Appl
PMCID: 5638085
PMID: 28488344
DOI: 10.1002/prca.201700015

[…] tion and Integrated Discovery (DAVID) version 6.8 was used for functional annotation , STRING version 10.0 for protein–protein interaction analysis , TMHMM Server v. 2.0 for membrane association, the Plasma Proteome Database used for comparison with the NAF proteome, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to identify metabolic pathways, and the Early Detection Research Network […]

call_split

An Evaluation of Blood Compatibility of Silver Nanoparticles

2016
Sci Rep
PMCID: 4857076
PMID: 27145858
DOI: 10.1038/srep25518
call_split See protocol

[…] ns and their interactions network were performed by Cytoscape plugged ClueGO + CluePedia with P-values (Bonferroni step down correction) <0.05. The concentrations of plasma proteins were derived from Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/). For correlation analysis of corona proteins’ pI and MW with their LFQ intensity, two tailed Spearman test was used. […]

library_books

Proteomic Analysis of Polypeptides Captured from Blood during Extracorporeal Albumin Dialysis in Patients with Cholestasis and Resistant Pruritus

2011
PLoS One
PMCID: 3136480
PMID: 21779339
DOI: 10.1371/journal.pone.0021850

[…] hat were unique to the extract derived from patient treatment was richer in proteins of low molecular weight than the set of proteins identified in albumin control samples or those expected from the plasma proteome database (http://plasmaproteomedatabase.org) (). A large fraction of these proteins (41%) corresponds to small molecules, with a molecular mass below 20 kDa, that were present in relat […]

Citations

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PPD institution(s)
Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India; Amrita School of Biotechnology, Amrita University, Kollam, Kerala, India; Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India; Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, India; Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India; Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India; Government Medical College, Bhavnagar, Gujarat, India; Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, Maharashtra, India; The Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Internal Medicine, Armed Forces Medical College, Pune, Maharashtra, India; Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India; Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD, USA; Department of Pathology, Johns Hopkins University, Baltimore, MD, USA

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