title: "Controlled, cross-species dataset for exploring biases in genome annotation and modification profiles".
abstract: Since the sequencing of the honey bee genome, proteomics by mass spectrometry has become increasingly popular for biological analyses of this insect; but we have observed that the number of honey bee protein identifications is consistently low compared to other organisms [1]. In this dataset, we use nanoelectrospray ionization-coupled liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to systematically investigate the root cause of low honey bee proteome coverage. To this end, we present here data from three key experiments: a controlled, cross-species analyses of samples from Apis mellifera, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Mus musculus and Homo sapiens; a proteomic analysis of an individual honey bee whose genome was also sequenced; and a cross-tissue honey bee proteome comparison. The cross-species dataset was interrogated to determine relative proteome coverages between species, and the other two datasets were used to search for polymorphic sequences and to compare protein cleavage profiles, respectively.
authors.affiliation: Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology and Centre for Sustainable Food Systems, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada V6T 1Z4.
authors.forename: Alison
authors.initials: A
authors.lastname: McAfee
authors.affiliation: Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology and Centre for Sustainable Food Systems, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada V6T 1Z4.
authors.forename: Sarah
authors.initials: S
authors.lastname: Michaud
authors.affiliation: Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology and Centre for Sustainable Food Systems, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada V6T 1Z4.
authors.forename: Leonard J
authors.initials: LJ
authors.lastname: Foster
keywords: Apis mellifera; Mass spectrometry; Nanoelectrospray ionization; Proteome coverage; Proteomics