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Nucleic Acids Res. 2014 Jan;42(Database issue):D959-65. doi: 10.1093/nar/gkt1251. Epub 2013 Dec 3.

Plasma Proteome Database as a resource for proteomics research: 2014 update.

Author information

1
Institute of Bioinformatics, International Technology Park, Bangalore 560 066, Karnataka, India, Amrita School of Biotechnology, Amrita University, Kollam 690 525, Kerala, India, Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India, Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India, Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bangalore 560 022, Karnataka, India, Department of Biotechnology, Kuvempu University, Shankaraghatta 577 451, Karnataka, India, Government Medical College, Bhavnagar 364 001, Gujarat, India, Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha 442 012, Maharashtra, India, The Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA, Department of Internal Medicine, Armed Forces Medical College, Pune 411 040, Maharashtra, India, Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore 560 022, Karnataka, India, Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3084, Australia, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA, Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA, Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA and Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA.

Abstract

Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/) was initially described in the year 2005 as a part of Human Proteome Organization's (HUPO's) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10,546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set. We believe that PPD will facilitate both clinical and basic research by serving as a comprehensive reference of plasma proteins in humans and accelerate biomarker discovery and translation efforts.

PMID:
24304897
PMCID:
PMC3965042
DOI:
10.1093/nar/gkt1251
[Indexed for MEDLINE]
Free PMC Article
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