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.

Exploring the potential of public proteomics data

“…More specific databases have also been established, related to: diseases, for example TBDB for tuberculosis 9; organisms, for example ProteomicsDB 10 and the Human Proteome Map 11 for the human proteome, and pep2pro for Arabidopsis 12; or subproteomes, for example CSF‐PR 13 for cerebrospinal fluid or TOPPR 14 and TopFIND 15 for in vivo cleaved proteins. For a comprehensive overview of the current proteomics databases and repositories, please see Perez‐Riverol et al 16.…”

A Smart Way for Talking With Proteins; Proteomics

“…And also researchers have different interest and research projects on proteomics data. 48 And one of the major challenges of global proteomic studies that we have faced with is the missing data, because many statistical approaches are not sufficient since they require complete datasets. 49 However, the importance of the data standardization, storage and sharing publicly has been increased.…”

“…Proteome Central has metadata associated with datasets [PRIDE and MassIVE for MS/MS data, PASSEL for SRM data, or Peptide Atlas for reprocessed original PX datasets]. 48 PRIDE 52 has peptide/protein identifications including PTMs, expression values, the analyzed mass spectra, and the related metadata. PRIDE supports both complete and partial submissions and data are stored as originally analyzed by the researchers.…”

“…60 has been formed and PRIDE, Peptide Atlas, PASSEL, and MassIVE are the active members of this consortium. 48 The PX consortium has been created for to generate collaboration and integration of research on MS proteomics repositories, proteomics researchers, and representatives from journals. Two major workflows -MS/MS and SRM methods-are fully supported in PX.…”

“…Peptide Atlas is one of the biggest and well-curated protein expression data resources. 48 Proteomics DB 53 is a human protein expression database storing protein and peptide identifications and quantification measurements. It contains information of over 18 000 human genes, representing around 90% of the human proteome.…”