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Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas
Nichole L King, Eric W Deutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B Martin, Bong Kim, Hookeun Lee, Brian Raught, Ruedi Aebersold
Genome Biol. 2006; 7(11): R106. Published online 2006 November 13. doi: 10.1186/gb-2006-7-11-r106
PMCID:
PMC1794584
Abstract Full Text PDF–1.3M Supplementary Material
 Is Cited by the Following 10 Articles in this Archive:
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
Alexey I. Nesvizhskii
J Proteomics. Author manuscript; available in PMC 2011 October 10.
Published in final edited form as: J Proteomics. 2010 October 10; 73(11): 2092–2123. Published online 2010 September 8. doi: 10.1016/j.jprot.2010.08.009
PMCID:
PMC2956504
Abstract Full Text PDF–3.5M
The PeptideAtlas Project
Eric W. Deutsch
Methods Mol Biol. Author manuscript; available in PMC 2011 April 14.
Published in final edited form as: Methods Mol Biol. 2010; 604: 285–296. doi: 10.1007/978-1-60761-444-9_19
PMCID:
PMC3076596
Abstract Full Text PDF–283K
Proteomics data repositories
Michael Riffle, Jimmy K. Eng
Proteomics. Author manuscript; available in PMC 2010 July 22.
Published in final edited form as: Proteomics. 2009 October; 9(20): 4653–4663. doi: 10.1002/pmic.200900216
PMCID:
PMC2908408
Abstract Full Text PDF–5.1M
Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry
Lukas Reiter, Manfred Claassen, Sabine P. Schrimpf, Marko Jovanovic, Alexander Schmidt, Joachim M. Buhmann, Michael O. Hengartner, Ruedi Aebersold
Mol Cell Proteomics. 2009 November; 8(11): 2405–2417. Published online 2009 July 16. doi: 10.1074/mcp.M900317-MCP200
PMCID:
PMC2773710
Abstract Full Text Supplementary Material
Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
Amol Prakash, Daniela M. Tomazela, Barbara Frewen, Brendan MacLean, Gennifer Merrihew, Scott Peterman, Michael J. MacCoss
J Proteome Res. Author manuscript; available in PMC 2010 June 1.
Published in final edited form as: J Proteome Res. 2009 June; 8(6): 2733–2739. doi: 10.1021/pr801028b
PMCID:
PMC2743471
Abstract Full Text PDF–1.2M Supplementary Material
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, The FlyBase Consortium, Ruedi Aebersold, Ernst Hafen
BMC Bioinformatics. 2009; 10: 59. Published online 2009 February 11. doi: 10.1186/1471-2105-10-59
PMCID:
PMC2648944
Abstract Full Text PDF–665K Supplementary Material
Comparison of MS2-only, MSA, and MS2/MS3 Methodologies for Phosphopeptide Identification
Peter J. Ulintz, Anastasia K. Yocum, Bernd Bodenmiller, Ruedi Aebersold, Philip C. Andrews, Alexey I. Nesvizhskii
J Proteome Res. Author manuscript; available in PMC 2010 February 1.
Published in final edited form as: J Proteome Res. 2009 February; 8(2): 887–899. doi: 10.1021/pr800535h
PMCID:
PMC2734953
Abstract Full Text PDF–2.5M
Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring
Vinzenz Lange, Johan A. Malmström, John Didion, Nichole L. King, Björn P. Johansson, Juliane Schäfer, Jonathan Rameseder, Chee-Hong Wong, Eric W. Deutsch, Mi-Youn Brusniak, Peter Bühlmann, Lars Björck, Bruno Domon, Ruedi Aebersold
Mol Cell Proteomics. 2008 August; 7(8): 1489–1500. doi: 10.1074/mcp.M800032-MCP200
PMCID:
PMC2494906
Abstract Full Text Supplementary Material
Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics
Phu T. Van, Amy K. Schmid, Nichole L. King, Amardeep Kaur, Min Pan, Kenia Whitehead, Tie Koide, Marc T. Facciotti, Young-Ah Goo, Eric W. Deutsch, David J. Reiss, Parag Mallick, Nitin S. Baliga
J Proteome Res. Author manuscript; available in PMC 2009 September 1.
Published in final edited form as: J Proteome Res. 2008 September; 7(9): 3755–3764. Published online 2008 July 25. doi: 10.1021/pr800031f
PMCID:
PMC2643335
Abstract Full Text PDF–585K Supplementary Material
Advances in proteomic workflows for systems biology
Johan Malmström, Hookeun Lee, Ruedi Aebersold
Curr Opin Biotechnol. Author manuscript; available in PMC 2008 August 1.
Published in final edited form as: Curr Opin Biotechnol. 2007 August; 18(4): 378–384. Published online 2007 August 14. doi: 10.1016/j.copbio.2007.07.005
PMCID:
PMC2048812
Abstract Full Text PDF–434K
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