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

Vishalakshi Nanjappa, Joji Kurian Thomas, Arivusudar Marimuthu, Babylakshmi Muthusamy, Aneesha Radhakrishnan, Rakesh Sharma, Aafaque Ahmad Khan, Lavanya Balakrishnan, Nandini A. Sahasrabuddhe, Satwant Kumar, Binit Nitinbhai Jhaveri, Kaushal Vinaykumar Sheth, Ramesh Kumar Khatana, Patrick G. Shaw, Srinivas Manda Srikanth, Premendu P. Mathur, Subramanian Shankar, Dindagur Nagaraja, Rita Christopher, Suresh MathivananRajesh Raju, Ravi Sirdeshmukh, Aditi Chatterjee, Richard J. Simpson, H. C. Harsha, Akhilesh Pandey, T. S.Keshava Prasad

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)D959-D965
JournalNucleic acids research
Volume42
Issue numberD1
DOIs
StatePublished - Jan 1 2014

ASJC Scopus subject areas

  • Genetics

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    Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Ahmad Khan, A., Balakrishnan, L., Sahasrabuddhe, N. A., Kumar, S., Jhaveri, B. N., Sheth, K. V., Kumar Khatana, R., Shaw, P. G., Srikanth, S. M., Mathur, P. P., Shankar, S., Nagaraja, D., Christopher, R., ... Prasad, T. S. K. (2014). Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic acids research, 42(D1), D959-D965. https://doi.org/10.1093/nar/gkt1251