Caister Academic Press

Standardized Formats, Report Information Guidelines, Mass Spectrometry-based Repositories and Application Programming Interfaces for Implementing Data Standards in Proteomics

J. Alberto Medina-Aunon and Juan P. Albar
from: Proteomics: Targeted Technology, Innovations and Applications (Edited by: Manuel Fuentes and Joshua LaBaer). Caister Academic Press, U.K. (2014)


This chapter focuses on the standardization of proteomics data. Sharing and detailed description of proteomics experimental results to enable verification by other scientists are fundamental principles of scientific research. However, the vast heterogeneity of data formats provided by equipment vendors has hindered the progress in this field, making difficult the verification of published results. The Human Proteome Organization initiative on proteomics standards (HUPO-PSI) has worked on the definition of standards for proteomics data representation as well as in the description of the guidelines that state the minimum information that should be included when reporting a proteomics experiment (MIAPE). Such minimum information must describe the complete experiment, including both experimental protocols and data processing methods, allowing a critical evaluation of the whole process and the potential repetition of the work. In this chapter we describe the standardization work performed by the HUPO-PSI, focusing on the MIAPE guidelines and the XML data formats. In addition, main proteomics data repositories are described as well as the application programming interphases (APIs) required for the integration of data standards into laboratory pipelines. Finally, bioinformatics tools for converting raw data into proteomics data standards and data analysis tools for inspection, validation, reporting and statistics are analyzed read more ...
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