Abstract
Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae) and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (PXD002319-PXD002328), PPIs via BioGRID (185267); and interaction network projections via (http://metazoa.med.utoronto.ca) made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1].
Highlights
Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens
The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1]
Set of tables Biochemical fractionation combined with quantitative mass spectrometry using LTQ XL; LTQ Orbitrap Velos Raw and processed data Whole body lysate from worm (Caenorhabditis elegans) AX4 cells from amoeba (Dictyostelium discoideum) 2 cell types in fly (Drosophila melanogaster), 5 cell lines in human (Homo sapiens), Embryonic stem cells from mice (Mus musculus) Unfertilized sea anemone eggs (Nematostella vectensis) Log-phase culture of wild type yeast W303 strain (Saccharomyces cerevisiae) 5 different development stages in sea urchin (Strongylocentrotus purpuratus), Stage 15–19 embryos, adult male heart and liver from frog (Xenopus laevis) Combination of biochemical fractionation with quantitative mass spectrometry for 6387 fractions obtained from 69 different experiments, to examine the composition of soluble multiprotein complexes among diverse animal models
Summary
Set of tables Biochemical fractionation combined with quantitative mass spectrometry using LTQ XL; LTQ Orbitrap Velos Raw and processed data Whole body lysate from worm (Caenorhabditis elegans) AX4 cells from amoeba (Dictyostelium discoideum) 2 cell types in fly (Drosophila melanogaster), 5 cell lines in human (Homo sapiens), Embryonic stem cells from mice (Mus musculus) Unfertilized sea anemone eggs (Nematostella vectensis) Log-phase culture of wild type yeast W303 strain (Saccharomyces cerevisiae) 5 different development stages in sea urchin (Strongylocentrotus purpuratus), Stage 15–19 embryos, adult male heart and liver from frog (Xenopus laevis) Combination of biochemical fractionation with quantitative mass spectrometry for 6387 fractions obtained from 69 different experiments, to examine the composition of soluble multiprotein complexes among diverse animal models. Functional analysis subsequently revealed metazoan-specific complexes responsible for cell–cell communication, development and disease, and ancient complexes extant for $ 1 billion years with central housekeeping roles. This reconstructed physical interaction network provides mechanistic insights into the unique organization and evolution of animal cells. We selected 5 human cell lines, 2 cell types in fly, and cells from 5 different development stages in sea urchin, along with whole body lysate from worm and embryonic stem cells from mice These 5 species were used in deriving interactions and complexes, while 4 additional species were subjected to the same preparation and quantitation methods, but used only in validation: frog, sea anemone, yeast and amoeba. The species, cell types, and fractionation methods used are provided as Supplementary information with the research article
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