A Bovine PeptideAtlas of milk and mammary gland proteomes

Proteomics

Volumn 12, Issue 18, 2012, Pages 2895-2899

  Bislev, Stine L ^a   Deutsch, Eric W ^b   Sun, Zhi ^b   Farrah, Terry ^b   Aebersold, Ruedi ^c,d   Moritz, Robert L ^b   Bendixen, Emøke ^a   Codrea, Marius C ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^c ETH ZURICH   (Switzerland)

^d UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Animal proteomics; Bos taurus; Mammary gland proteome; Milk proteome; PeptideAtlas; Proteotypic peptides

Indexed keywords

PROTEOME;

ANIMAL TISSUE; ARTICLE; BOS TAURUS; COW; FARM ANIMAL; GENE MAPPING; MAMMARY GLAND; MILK PRODUCTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SPECTRUM;

AMINO ACID SEQUENCE; ANIMALS; CATTLE; DATABASES, PROTEIN; FEMALE; HAPTOGLOBINS; MAMMARY GLANDS, ANIMAL; MILK; MOLECULAR SEQUENCE DATA; PROTEOME; PROTEOMICS;

ANIMALIA; BOS TAURUS; BOVINAE;

EID: 84866163561     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200057     Document Type: Article

References (23)

1. Vizcaino, J. A., Cote, R., Reisinger, F., Foster, J. M. et al., A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 2009, 9, 4276-4283.
2. Craig, R., Cortens, J. P., Beavis, R. C., Open source system for analyzing, validating, and storing protein identification data. J. Proteome. Res. 2004, 3, 1234-1242.
3. Falkner, J. A., Andrews, P. C., P6-T Tranche: secure decentralized data storage for the proteomics community. J. Biomol. Tech 2007, 18, 3.
4. Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
5. Vizcaino, J. A., Foster, J. M., Martens, L., Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J. Proteomics. 2010, 73, 2136-2146.
6. Bendixen, E., Danielsen, M., Hollung, K., Gianazza, E. et al., Farm animal proteomics-a review. J. Proteomics 2011, 74, 282-293.
7. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I. et al., The PeptideAtlas project. Nucleic Acids Res. 2006, 34, D655-D658.
8. King, N. L., Deutsch, E. W., Ranish, J. A., Nesvizhskii, A. I. et al., Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol. 2006, 7, R106.
9. Loevenich, S. N., Brunner, E., King, N. L., Deutsch, E. W. et al., The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC. Bioinformatics 2009, 10, 59.
10. Chan, Q. W., Parker, R., Sun, Z., Deutsch, E. W. et al., A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues. BMC. Genomics 2011, 12, 290.
11. Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B. et al., Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 2009, 138, 795-806.
12. Danscher, A. M., Toelboell, T. H., Wattle, O. Biomechanics and histology of bovine claw suspensory tissue in early acute laminitis. J. Dairy Sci. 2010, 93, 53-62.
13. Danielsen, M., Codrea, M. C., Ingvartsen, K. L., Friggens, N. C. et al., Quantitative milk proteomics-host responses to lipopolysaccharide-mediated inflammation of bovine mammary gland. Proteomics 2010, 10, 2240-2249.
14. Bislev, S. L., Kusebauch, U., Codrea, M. C., Beynon, R. J. et al., Quantotypic properties of QconCAT peptides targeting bovine host response to Streptococcus uberis. J. Proteome Res. 2012, 11, 1832-1843.
15. Farrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S. et al., A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell Proteomics 2011, 10, M110.
16. Martens, L., Chambers, M., Sturm, M., Kessner, D. et al., mzML-a community standard for mass spectrometry data. Mol. Cell Proteomics 2011, 10, R110.
17. Kessner, D., Chambers, M., Burke, R., Agus, D. et al., ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24, 2534-2536.
18. Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
19. MacLean, B., Eng, J. K., Beavis, R. C., McIntosh, M., General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 2006, 22, 2830-2832.
20. Keller, A., Eng, J., Zhang, N., Li, X. J. et al., A uniform proteomics MS/MSanalysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 1-8.
21. Nesvizhskii, A. I., Keller, A., Kolker, E., Aebersold, R., A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75, 4646-4658.
22. Farrah, T., Deutsch, E. W., Aebersold, R., Using the human plasma PeptideAtlas to study human plasma proteins. Methods Mol. Biol. 2011, 728, 349-374.
23. Elsik, C. G., Tellam, R. L., Worley, K. C., Gibbs, R. A. et al., The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324, 522-528.