Development of data representation standards by the human proteome organization proteomics standards initiative

Abstract

Objective To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI’s evolution, and future directions and synergies for the group.Materials and Methods The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release.Results We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

“…Each set of guidelines has been distinct in its focus and goals; no single set of guidelines is applicable to all goals. The Minimum Information About a Proteomics Experiment (MIAPE) guidelines 11 developed by the HUPO Proteomics Standards Initiative (PSI) 12 focus specifically on the metadata annotation of experimental MS results. These metadata must describe what was done to execute the experiment with sufficient detail that the results may be properly interpreted or reproduced; MIAPE explicitly does not stipulate how an analysis is to be performed.…”

An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results

“…The HUPO Proteomics Standards Initiative [27–28], has defined several open formats that allow data and results from many different instruments and pipelines to be represented in a common language. The current standard for database search results, mzIdentML, does not support cross-linked PSMs at the time of this writing.…”

ProCon — PROteomics CONversion tool

“…These modifications definitions are then mapped to the corresponding PRIDE resp. PSI-MS CV [9] (Controlled Vocabulary) terms. The conversion to the PRIDE XML format is done by instantiating objects from the PRIDE_core_2_5_4.jar library from the EBI (European Bioinformatics Institute).…”

“…Furthermore, the assessment of the performance of newly developed software algorithms analyzing the data is made easier by having access to the data in such data repositories. These XML-based formats defined by the HUPO-PSI working group [8,9] incorporate also semantic annotations of the data by the use of controlled vocabulary terms from a set of ontologies [10,11]. The use of these ontology terms ensures that standardized terms are used and thereby avoids problems resulting from the usage of synonyms, the use of capital and small initial letters and misspellings.…”