Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays

Bioinformatics, vol. 37, pp. 1900–1908

Abstract

MotivationLaboratory mouse is the most used animal model in biological research, largely due to its high conserved synteny with human. Researchers use mice to answer various questions ranging from determining a pathological effect of knocked out/in gene to understanding drug metabolism. Our group developed >5000 quantitative targeted proteomics assays for 20 mouse tissues and determined the concentration ranges of a total of >1600 proteins using heavy labeled internal standards. We describe here MouseQuaPro; a knowledgebase that hosts this collection of carefully curated experimental data. ResultsThe web-based application includes protein concentrations from >700 mouse tissue samples from three common research strains, corresponding to >200k experimentally determined concentrations. The knowledgebase integrates the assay and protein concentration information with their human orthologs, functional and molecular annotations, biological pathways, related human diseases and known gene expressions. At its core are the protein concentration ranges, which provide insights into (dis)similarities between tissues, strains and sexes. MouseQuaPro implements advanced search as well as filtering functionalities with a simple interface and interactive visualization. This information-rich resource provides an initial map of protein absolute concentration in mouse tissues and allows guided design of proteomics phenotyping experiments. The knowledgebase is available on mousequapro.proteincentre.com. AVAILABILITY AND IMPLEMENTATION: The knowledgebase is available free of charge on http://mousequapro.proteincentre.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors 5

1. Yassene Mohammed corresponding Aachen Center for Proteomics and Metabolomics

   University of Victoria · Leiden University Medical Center · Genome British Columbia

   Affiliation as printed

   Center for Proteomics and Metabolomics , Leiden University Medical Center, Leiden 2333 ZA, The Netherlands

   University of Victoria — Genome British Columbia Proteomics Centre , University of Victoria, Victoria, BC V8Z 7X8, Canada

2. Pallab Bhowmick

   University of Victoria · Genome British Columbia

   Affiliation as printed

   University of Victoria — Genome British Columbia Proteomics Centre , University of Victoria, Victoria, BC V8Z 7X8, Canada

3. Sarah A. Michaud

   University of Victoria · Genome British Columbia

   Affiliation as printed

   University of Victoria — Genome British Columbia Proteomics Centre , University of Victoria, Victoria, BC V8Z 7X8, Canada

4. Albert Sickmann

   Leibniz Institute for Analytical Sciences - ISAS

   Affiliation as printed

   Leibniz Institut für Analytische Wissenschaften—ISAS—e.V ., Dortmund 44227, Germany

5. Christoph H. Borchers

   Skolkovo Institute of Science and Technology · Jewish General Hospital · Lady Davis Institute for Medical Research · McGill University

   Affiliation as printed

   Center for Computational and Data-Intensive Science and Engineering , Skolkovo Institute of Science and Technology, Moscow 121205, Russia

   Gerald Bronfman Department of Oncology , Jewish General Hospital, Montreal, QC H4A 3T2, Canada

   Proteomics Centre, Segal Cancer Centre, Lady Davis Institute , Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada