Engineering a proteomics pipeline for the cellmap project

Summary form only given. Proteomics, focuses on the identification, localization, and functional analysis of the protein make up of the cell. It evolved from genomics, where the focus is on the information of one target molecule DNA. Genomics involves the high throughput sequencing of DNA and the subsequent data storage and annotation; the process is complex but there is only one genome for each organism. In contrast, the proteins present in a cell, together with their function, sub-cellular location, and structure change dramatically with the organ, and the conditions faced by their host cells including: age, checkpoint in the cell cycle, and external or internal signaling events. Thus, there will be many proteomes for each organism and consequently, the quantity and complexity of proteomics data will be orders of magnitude greater genomic data. Acquiring, analyzing, and interpreting these vast data sets requires a robust proteomics pipeline that integrates a series of high-throughput technologies to lead the researcher from experimental design to biological insight. Engineering this proteomics pipeline requires the integrated application of information technology, biomedical engineering, and bioinformatics to implement individual analyses, link the different stages together, maximize throughput, optimize the information extracted from the data, and provide a comprehensive overview of the results. Moreover, since proteomics is inherently collaborative, the proteomics pipeline must provide for the flow of information to and from researchers working at different stages of one project or different projects. The Montreal Proteomics network is undertaking ambitious project which aims to characterize the proteome(s) of the organelles that make up the mammalian cell. This paper will define the functional requirements of the proteomics pipeline required to support this project and describe the hardware/software architecture and implementation strategy adopted. It will then discuss key elements of the current pipeline, document its performance, and describe ongoing research aimed at improving its accuracy and throughput. Finally, it will describe how new technologies can be expected to impact the proteomics pipelines.