Human Proteinpedia: a unified discovery resource for proteomics research

Abstract

Sharing proteomic data with the biomedical community through a unified proteomic resource, especially in the context of individual proteins, is a challenging prospect. We have developed a community portal, designated as Human Proteinpedia (http://www.humanproteinpedia.org/), for sharing both unpublished and published human proteomic data through the use of a distributed annotation system designed specifically for this purpose. This system allows laboratories to contribute and maintain protein annotations, which are also mapped to the corresponding proteins through the Human Protein Reference Database (HPRD; http://www.hprd.org/). Thus, it is possible to visualize data pertaining to experimentally validated posttranslational modifications (PTMs), protein isoforms, protein–protein interactions (PPIs), tissue expression, expression in cell lines, subcellular localization and enzyme substrates in the context of individual proteins. With enthusiastic participation of the proteomics community, the past 15 months have witnessed data contributions from more than 75 labs around the world including 2710 distinct experiments, >1.9 million peptides, >4.8 million MS/MS spectra, 150 368 protein expression annotations, 17 410 PTMs, 34 624 PPIs and 2906 subcellular localization annotations. Human Proteinpedia should serve as an integrated platform to store, integrate and disseminate such proteomic data and is inching towards evolving into a unified human proteomics resource.

SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome

“…We also searched for previous reports describing detection of these proteins in any biological fluids, using HPRD and the Human proteinpedia (HUPA; www.humanproteinpedia.org). 40 Of the 441 proteins identified, 72 contained signal peptides (SP), 11 contained a transmembrane (TM) domain and 15 contained both a TM domain and an SP motif. The MS and MS/MS spectra of representative known and novel proteins are displayed in Figure 3.…”

“…40 The ESCC secretome dataset generated using qTOF is freely available for use in its entirety from ProteomeCommons.org. On-line versions of the data may be found at www.proteomecommons.org/member-data.jsp?i = 657 or by searching on the keyword "ESCC Secretome" from the proteomecommons.org main page or alternatively it can be located in the Tranche data repository and can be downloaded from Tranche data repository using "S/ BvVTpUE09k0gNOjAP6lbQKxiAzpsd/f92Lu0KfU61Pzoxnb-GPiS9Hn5EqL3BhAl9HD2 + LReVGAGnoI9QSTFDkaJfAA AAAAABGKwg==" and "Do7AlAhIJBy + TBAJeGbOQ9 MmFprHZQU0cdK1wTzpLcFExjQ/L5xM6CanLJfgQB + Prdx jbetyxvSdy8ijsXCC + Jyk4HEAAAAAAAEdmA==" hash.…”

Proteomic-Based Approach To Gain Insight into Reprogramming of THP-1 Cells Exposed to Leishmania donovani over an Early Temporal Window

“…To make our findings publicly available and accessible to the research community, we have submitted our quantification data and the list of proteins and peptides identified to the Human Proteinpedia (HUPA) (http://www .humanproteinpedia.org/) (26,27). The data (accession number HuPA_00807) can be freely downloaded from the following links: http: //www.humanproteinpedia.org/data_display?exp_idϭ00807 for experiment details and http://www.humanproteinpedia.org/download_data?…”

Human Protein Reference Database and Human Proteinpedia as Discovery Resources for Molecular Biotechnology

“…Human Proteinpedia [91,92] is a proteomic database with a public distribution annotation system where proteomic investigators can share experimental data with biomedical community by submitting the information into a centralized repository. Human Proteinpedia utilizes HPRD as a scaffold in which the submitted proteomic information is mapped to corresponding protein features and is reflected in a separate table in protein pages of HPRD [93].…”