Making proteomics data accessible and reusable: current state of proteomics databases and repositories

Abstract

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data.

Keywords: Bioinformatics; Databases; MS; Repositories.

Figure 1

Hierarchy of proteomics data repositories and databases according to the different data types stored: raw MS data repositories, resources that store peptide/protein identification and quantification results, and protein knowledge bases. Some resources are duplicated in different levels because they can be included in more than one category.

Figure 2

Bubble chart representation of the size of the PX complete submissions to PRIDE (until May 2014). The x-axis includes months with at least one submission, since PX submissions started (from March 2012). The y-axis corresponds to the number of PX “complete” public datasets submitted to PRIDE in each specific month. The size of each bubble represents the total number of mass spectra included in all the datasets in a given month.

Figure 3

(A) Number of UniProtKB/Swiss-Prot human proteins (release 2014_05, 20,265 entries) observed in different proteomics resources that have a uniform data processing pipeline (GPMDB, ProteomicsDB, PeptideAtlas, HPM, PaxDb, MaxQB, Human Proteinpedia; PRIDE is not included); (B) Venn diagram representing the human protein identifications observed in GPMDB, PeptideAtlas, and ProteomicsDB; (C) Area chart showing the distribution of the number of PRIDE assays for those proteins present in three, two, and one proteomics resources, or for those proteins not identified at all.