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Items: 12

1.

Genome annotation of a Saccharomyces sp. lager brewer's yeast.

De León-Medina PM, Elizondo-González R, Damas-Buenrostro LC, Geertman JM, Van den Broek M, Galán-Wong LJ, Ortiz-López R, Pereyra-Alférez B.

Genom Data. 2016 May 21;9:25-9. doi: 10.1016/j.gdata.2016.05.009. eCollection 2016 Sep.

2.

Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline.

Zhu X, Xie S, Armengaud J, Xie W, Guo Z, Kang S, Wu Q, Wang S, Xia J, He R, Zhang Y.

Mol Cell Proteomics. 2016 Jun;15(6):1791-807. doi: 10.1074/mcp.M115.050989. Epub 2016 Feb 22.

3.

Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry.

Nagarajha Selvan LD, Kaviyil JE, Nirujogi RS, Muthusamy B, Puttamallesh VN, Subbannayya T, Syed N, Radhakrishnan A, Kelkar DS, Ahmad S, Pinto SM, Kumar P, Madugundu AK, Nair B, Chatterjee A, Pandey A, Ravikumar R, Gowda H, Prasad TS.

Clin Proteomics. 2014 Feb 3;11(1):5. doi: 10.1186/1559-0275-11-5.

4.

A proteogenomic survey of the Medicago truncatula genome.

Volkening JD, Bailey DJ, Rose CM, Grimsrud PA, Howes-Podoll M, Venkateshwaran M, Westphall MS, Ané JM, Coon JJ, Sussman MR.

Mol Cell Proteomics. 2012 Oct;11(10):933-44. Epub 2012 Jul 5.

5.

Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification.

Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.

J Proteome Res. 2012 Mar 2;11(3):1621-32. doi: 10.1021/pr2008175. Epub 2012 Feb 21.

6.

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium.

Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN.

BMC Genomics. 2011 Aug 25;12:433. doi: 10.1186/1471-2164-12-433.

7.

OryzaPG-DB: rice proteome database based on shotgun proteogenomics.

Helmy M, Tomita M, Ishihama Y.

BMC Plant Biol. 2011 Apr 12;11:63. doi: 10.1186/1471-2229-11-63.

8.

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data.

Braaksma M, Martens-Uzunova ES, Punt PJ, Schaap PJ.

BMC Genomics. 2010 Oct 19;11:584. doi: 10.1186/1471-2164-11-584.

9.

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.

Nesvizhskii AI.

J Proteomics. 2010 Oct 10;73(11):2092-123. doi: 10.1016/j.jprot.2010.08.009. Epub 2010 Sep 8. Review.

10.

Investigating protein isoforms via proteomics: a feasibility study.

Blakeley P, Siepen JA, Lawless C, Hubbard SJ.

Proteomics. 2010 Mar;10(6):1127-40. doi: 10.1002/pmic.200900445.

11.

Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.

Baudet M, Ortet P, Gaillard JC, Fernandez B, Guérin P, Enjalbal C, Subra G, de Groot A, Barakat M, Dedieu A, Armengaud J.

Mol Cell Proteomics. 2010 Feb;9(2):415-26. doi: 10.1074/mcp.M900359-MCP200. Epub 2009 Oct 29.

12.

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum.

Bringans S, Hane JK, Casey T, Tan KC, Lipscombe R, Solomon PS, Oliver RP.

BMC Bioinformatics. 2009 Sep 22;10:301. doi: 10.1186/1471-2105-10-301.

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