Human Proteinpedia as a resource for clinical proteomics

Abstract

Clinical proteomics is an emerging field that deals with the use of proteomic technologies for medical applications. With a major objective of identifying proteins involved in pathological processes and as potential biomarkers, this field is already gaining momentum. Consequently, clinical proteomics data are being generated at a rapid pace, although mechanisms of sharing such data with the biomedical community lag far behind. Most of these data are either provided as supplementary information through journal web sites or directly made available by the authors through their own web resources. Integration of these data within a single resource that displays information in the context of individual proteins is likely to enhance the use of proteomic data in biomedical research. Human Proteinpedia is one such portal that unifies human proteomic data under a single banner. The goal of this resource is to ultimately capture and integrate all proteomic data obtained from individual studies on normal and diseased tissues. We anticipate that harnessing of these data will help prioritize experiments related to protein targets and also permit meta-analysis to uncover molecular signatures of disease. Finally, we encourage all biomedical investigators to maximize dissemination of their valuable proteomic data to rest of the community by active participation in existing repositories such as Human Proteinpedia.

Fig. 1.

Display of expression and subcellular localization of tumor protein D52-like 2 in HPRD molecule page. Molecule page of tumor protein D52-like 2 in HPRD is displayed. Almost all information for this protein is derived from community annotations through Human Proteinpedia including subcellular localization and expression in tissues, cell lines, and diseases. The annotated data shows that this molecule is expressed in B cells, brain, liver, ovary, and platelets. It is also expressed in ovarian cancer and in several cell lines (293T, HeLa, and K-562). Clicking on any of these hyperlinked terms opens a pop-up window (e.g. cytoplasm or platelet, as shown), which provides additional experimental data and details about the contributing laboratory as well as any publications. For example, the window on the left shows peptide identification data, peptide scores, precursor mass, charge state, and sequence identifiers from this unpublished study. If available, the MS/MS spectra are hyperlinked to another window as shown in the right lower part that allows the users to manually inspect the data.

Fig. 2.

Display of post-translational modifications and protein interactors for tumor protein D52-like 2. a, the molecule page for tumor protein D52-like 2 is shown with several interacting proteins manually annotated in HPRD and one protein, I-Kappa-B Kinase-Epsilon, based on data contributed to Human Proteinpedia from a mass spectrometry experiment. The experimental details along with information about the contributing laboratory are also shown. b, no curated post-translational modifications exist for this protein in HPRD. However, the Human Proteinpedia tab shows that there are two phosphorylation sites that have been contributed based on a published study. The lower panel provides a description of the experiment, phosphopeptides identified, and the peptide score.

Fig. 2.

Display of post-translational modifications and protein interactors for tumor protein D52-like 2. a, the molecule page for tumor protein D52-like 2 is shown with several interacting proteins manually annotated in HPRD and one protein, I-Kappa-B Kinase-Epsilon, based on data contributed to Human Proteinpedia from a mass spectrometry experiment. The experimental details along with information about the contributing laboratory are also shown. b, no curated post-translational modifications exist for this protein in HPRD. However, the Human Proteinpedia tab shows that there are two phosphorylation sites that have been contributed based on a published study. The lower panel provides a description of the experiment, phosphopeptides identified, and the peptide score.

Fig. 3.

SMEK1 expression in colon and colorectal cancer. SMEK1 molecule page is shown with links to the Human Proteinpedia page indicating expression in colon and colorectal cancer (highlighted), among other sites and diseases. Links from colon displays the experiment description and the information of the contributing group. Human protein atlas links are provided from the Human Proteinpedia page, which indicate moderate expression of SMEK1 in the glandular cells of normal colon tissue. A hyperlink from colorectal cancer again leads to the same resource, which reveals strong expression of SMEK1 in the tumor cells in colorectal cancer tissue.

Fig. 4.

FGL2 expression in hepatocellular carcinoma. The molecule page of FGL2, a secreted protein, is shown. Based on unpublished data submitted to Human Proteinpedia, there are two entries based on two different experimental platforms showing that it is expressed in HCC². Immunohistochemical staining shows that it is expressed in HCC; this is accompanied by information about the antibody used. The second entry shows that it is overexpressed based on Western blot analysis.² R. Chaerkady and A. Pandey, unpublished data.