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

TLDR

The Plasma Proteome Database, launched in 2005 as part of HUPO’s Human Plasma Proteome Project, has expanded with advances in proteomic technologies that have identified many novel plasma proteins. The authors aim to enrich PPD with updated proteomic data and provide a batch-based query tool, the Plasma Proteome Explorer, to help users assess the novelty of their protein or peptide lists. The database was updated by adding mass spectrometry‑derived data, verified proteotypic peptides, concentration values for 1,278 proteins, extracellular vesicle protein categories, and implementing a batch‑based query tool for novelty assessment. PPD now catalogs 10,546 proteins, with 3,784 reported in multiple studies, and includes mass spectrometry‑derived data, verified peptides, concentration values, and extracellular vesicle proteins, positioning it as a comprehensive reference to accelerate biomarker discovery.

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.