1. The database deals purely with proteins found in plasma and serum. Why was it necessary to create Plasma Proteome Database (PPD)?
  Plasma is the most commonly diagnosed clinical sample. Clinicians can diagnose pathological conditions by quantification of specific proteins. Over 9,000 proteins in plasma and serum have thus far been reported and are only expected to increase with evolving high-resolution and high-sensitivity protein detection/identification technologies. Documentation of qualitative and quantitative information on broad range of proteins in plasma/serum in a user-friendly and queryable manner is a prerequisite to explore the blood proteome. This is why the Plasma Proteome Database was created.
   
2. What is the information that one can get from Plasma proteome Database?
  PPD contains proteins reported in plasma and serum from healthy individuals. Experimental method employed to identify each protein is also provided. From studies employing mass spectrometry-based approaches to identify plasma/serum proteins, information pertaining to the type of mass spectrometer employed and the proteotypic peptides reported are available. Quantitative information on plasma/serum proteins from immunoassays such as ELISA and radioimmuno assay, and mass spectrometry-based assays such as single reaction monitoring/multiple reaction monitoring and spectral counting are also available in PPD. All the information is linked to their corresponding PubMed identifiers. Proteins identified in plasma exosomes along with other experimental details are also available in PPD.
   
3. Is the protein concentration provided only from healthy individuals?
  Yes. Plasma protein levels are provided in healthy conditions as reported in literature.
   
4. What are the applications of PPD?
  PPD can be used as a reference database to compare and report proteins or peptides novel to experimental results obtained by researchers. The proteotypic peptides cataloged in PPD can be used to design and evaluate proteins using mass spectrometry both qualitatively and quantitatively. The list of proteins in PPD can also be used to analyze proteins from other body fluids. The proteins thus far identified in plasma/serum would also provide a reference for analysis of cellular secretome, proteins shed from cell surface and screen for ligands of orphan receptors. Above all, PPD will enable researchers in biomarker development to screen candidate molecules that are reported in plasma/serum, from a larger set of proteins identified in the discovery phase to pursue further validation.
   
5. Can I download data from PPD?
  Yes. The data is available for free download in .XML and tab delimited formats for non-commercial use under Creative Commons License 2.5 which attributes unrestricted use, distribution, and reproduction in any medium, provided, adequate credit is given to the authors.
   
6. I am from a commercial entity what do I need to do to download the database for commercial purposes?
  Please send an e-mail.
   
7. Can I contribute to PPD?
  We welcome participation of the scientific community in any form to improve and update PPD. You can add plasma protein concentration by following the link (click here). In addition, you can also provide articles published by your group on plasma proteins through "Submit new articles" tab under "Publications" section. Our team will curate and review the data for inclusion in PPD.
   
8. Whom do I contact if I see an error?
  Please submit any comments through the web form under feedback tab.