Abstract
The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/.
Highlights
From the ‡Proteomics Facility, Centro Nacional de Biotecnología CSIC, Madrid, Spain; §Institute of Integrative Biology, University of Liverpool, Liverpool, UK
The analysis was based on a data-dependent experiment of the two most abundant ions in the survey scan in MS mode, alternating collision-induced dissociation (CID) and electron-transfer dissociation (ETD) fragmentation techniques in MS/MS mode
Its main characteristic is its ability to automatically translate and link data derived from proteomics experiments, using the current HUPO-PSI standards and MIAPE guidelines, saving significant effort and time for users
Summary
The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards*. The MIAPE modules and XML schemas are complementary resources—the MIAPE documents describe what information should be reported about an experimental technique (presented in a human readable format), and the XML schemas describe how such information can be captured in a format open to computational processing These contributions have been favorably received by the proteomics community, making data sharing and reporting less time-consuming for both experts and occasional users. As a contribution to this goal, the bioinformatics work group was created to improve computational analysis and communication among the different network partners It accepted HUPO-PSI guidelines regarding data sharing and reporting as the main way to exchange proteomics data among members of the ProteoRed network. We have developed a new web toolkit capable of linking the latest versions of the HUPOPSI XML schemas to the ProteoRed MIAPE web repository in an automated, accessible, and comprehensive way
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