Chan et al. BMC Genomics 2011, 12:290 http://www.biomedcentral.com/1471-2164/12/290 Abbreviations BLAST: Basic Local Alignment Search Tool; EST: expressed sequence tags; FDR: false discovery rate; GO: Gene Ontology; HBPA: Honey Bee PeptideAtlas; HSP: high-scoring segment pair; MS: mass spectrometry; MS/MS: tandem mass spectrometry; ORF: open reading frame; SRM: single reaction monitoring; STAGE Tips: STop-And-Go Extraction tips Acknowledgements Collection of the bee MS/MS was funded by an NSERC Discovery Grant to LJF and various funding from Genome British Columbia, the British Columbia Honey Producers Association through the Boone-Hodgson-Wilkinson Fund, the Canadian Honey Council and Canadian Association of Professional Apiculturists through the Canadian Bee Research Fund, the British Columbia Blueberry Council, the British Columbia Cranberry Marketing Association and Agri-Food Canada’s Advancing Canadian Agriculture and Agri-Food (ACAAF) program. The latter is part of a Collective Outcome project with the cooperation of the Investment Agriculture Foundation of British Columbia, the Alberta Agriculture and Food Council, the Saskatchewan Council for Community Development, the Manitoba Rural Adaptation Council, the Ontario Agricultural Adaptation Council, the Conseil pour le développement de l’agriculture du Québec, and Agri-Futures Nova Scotia. Mass spectrometry infrastructure used in this project was supported by the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund and the British Columbia Proteomics Network (BCPN). LJF is the Canada Research Chair in Quantitative Proteomics. Funding for EWD and ZS for the PeptideAtlas construction was funded in part with federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract No. N01-HV-28179, and from the Duchy of Luxembourg Systems Biology Initiative. Author details 1Centre for High-Throughput Biology and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada. 2Institute for Systems Biology, Seattle, WA, USA. Authors’ contributions EWD and LJF conceived of the project idea. QWTC compiled the mass spectra for this study. QWTC did the proteogenomics analysis with help from RP. ZS processed the raw data to generate the Honey Bee PeptideAtlas. QWTC, EWD and LJF wrote the initial version of the manuscript. All authors have read and approved the final manuscript. Received: 15 February 2011 Accepted: 3 June 2011 Published: 3 June 2011 References 1. Consortium THGS: Insights into social insects from the genome of the honeybee Apis mellifera. Nature 2006, 443(7114):931-49. 2. Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM: Creating a honey bee consensus gene set. Genome Biol 2007, 8(1):R13. 3. 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