PXD002275

PXD002275 is an original dataset announced via ProteomeXchange.

Title	Towards an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics.
Description	The honey bee is a key pollinator in many agricultural operations as well as a model organism for studying the genetics and evolution of social behaviour. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant aspects of their biology. One troubling trend that emerged from proteomic analyses is that honey bee peptide samples consistently result in lower peptide identification rates compared to other organisms. This suggests that the genome annotation can be improved, or atypical biological processes are interfering with the mass spectrometry workflow. First, we tested whether high levels of polymorphisms could explain some of the missed identifications by searching spectra against the reference proteome (OGSv3.2) versus a customized proteome of a single honey bee, but our results indicate that this contribution was minor. Likewise, error-tolerant peptide searches lead us to eliminate unexpected post-translational modifications as a major factor in missed identifications. We then used a proteogenomic approach with ~1,500 raw files to search for missing genes, new exons, and revive discarded annotations and identified over 2,000 new coding regions. These results will contribute to a more comprehensive genome annotation and facilitate continued research on this important insect.
HostingRepository	PRIDE
AnnounceDate	2016-01-18
AnnouncementXML	Submission_2016-01-18_04:46:26.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alison McAfee
SpeciesList	scientific name: Apis mellifera (Honeybee); NCBI TaxID: 7460; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive; Bruker Daltonics micrOTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-01 02:01:28	ID requested
⏵ 1	2016-01-18 04:46:27	announced

McAfee A, Harpur BA, Michaud S, Beavis RC, Kent CF, Zayed A, Foster LJ, Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics. J Proteome Res, 15(2):411-21(2016) [pubmed]

curator keyword: Biological

submitter keyword: Honey bees, Apis mellifera, gene annotation, mass spectrometry, proteogenomics

Leonard James Foster
contact affiliation	Department of Biochemistry and Molecular Biology, Center for High-throughput Biology, UBC, Vancouver, Canada
contact email	foster@chibi.ubc.ca
lab head
Alison McAfee
contact affiliation	UBC
contact email	alison.mcafee@alumni.ubc.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002275
     1. Label: PRIDE project
     2. Name: Towards an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics.