Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Eric W Deutsch,Shin Kawano,Henry Lam,Wout Bittremieux,Yasset Perez-Riverol,Gerben Menschaert,Mathias Walzer,Pierre-Alain Binz,Juan Antonio Vizcaíno,Reza M Salek,Sandra Orchard,Stefan Tenzer,Gerhard Mayer,David L Tabb,Henning Hermjakob,Andrew R Jones,Martin Eisenacher

doi:10.1021/acs.jproteome.7b00370

Abstract

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

Highlights

Application of proteomics technologies to identify proteins present in biological samples, measure their abundances, understand their functions, and determine their molecular interaction partners has become a common component of studies of complex biological systems in health and disease
We have reviewed the operations of the Proteomics Standards Initiative (PSI), the current status of the main existing standards, the plans for upcoming standards, and the synergies between the PSI, Metabolomics Standards Initiative (MSI), and other groups
With a full set of standard formats and minimum information guidelines for most data types relevant to proteomics already developed or soon emerging, what is left for the PSI to accomplish?

Summary

■ INTRODUCTION

Application of proteomics technologies to identify proteins present in biological samples, measure their abundances, understand their functions, and determine their molecular interaction partners has become a common component of studies of complex biological systems in health and disease. Several tools have been developed to compute QC metrics, these initiatives lack a unifying frame of reference, hindering the long-term maturation of MS QC To this end the Quality Control Working Group, the PSI’s most recently established working group, is undertaking efforts to establish a QC community standard.[51] This standard will consist of a formalized version of the qcML file format,[7] an associated CV, and a MIAPE-QC specification, along with corresponding resources to generate and aid interpretation of the QC information. It is envisioned that PROXI will be implemented at all of the major proteomics data repositories PRIDE,[18] Peptide Atlas,[58−60] MassIVE, and jPOST19 as well as the ProteomeCentral site (http://proteomecentral.proteomexchange.org/) of ProteomeXchange and other willing participants, allowing information access across all sites in a uniform manner This effort will rely substantially on the Universal Spectrum Identifier and PSI Spectrum Library Format standards described above. The PSI plays an important role in the Human Proteome Project,[63] the flagship project of HUPO, by helping to set standards for HPP contributions, such as the HPP MS Data Interpretation Guidelines, as already mentioned[36] (http://hupo.org/Guidelines)

■ CONCLUSIONS

■ ACKNOWLEDGMENTS

■ REFERENCES