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Workflow for investigating multispecies cardiac proteomes.

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posted on 06.09.2019 by Joel D. Federspiel, Panna Tandon, Caralynn M. Wilczewski, Lauren Wasson, Laura E. Herring, Samvida S. Venkatesh, Ileana M. Cristea, Frank L. Conlon

(A) Heart tissue from M. musculus, S. scrofa, X. laevis, and X. tropicalis was collected and subjected to differential protein extraction as detailed. The resulting 3 extracts were fractionated by SDS-PAGE. (B) Number of proteins identified in the 5 gel fractions for each extract (extract 1–3 from panel A) per species. These numbers include proteins found in 2 or more extracts. (C) PCA of MS1 proteome data demonstrates that the mammalian samples separate from each other and the Xenopus samples but the Xenopus samples maintain a tight association. (D) Data analysis workflow. (E) Identified proteins were mapped to human accession numbers using Blast2GO. (F) The shared proteins in all species represent a core cardiac proteome that is enriched for a variety of pathways. Shown here in a tree map are the top 10 most enriched (adjusted p ≤ 0.05) GO biological process terms; box size scales with enrichment significance of the terms. (G) Examples of proteins detected in subsets of the species analyzed. See S8 Table for numerical data underlying figure. GO, Gene Ontology; Kcp, Kielin/chordin-like protein; LC-MS/MS, liquid chromatography coupled with tandem mass spectrometry;MS1, precursor ion.

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