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Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
Lyris MF de Godoy, Jesper V Olsen, Gustavo A de Souza, Guoqing Li, Peter Mortensen, Matthias Mann
Genome Biol. 2006; 7(6): R50. Published online 2006 June 19. doi: 10.1186/gb-2006-7-6-r50
PMCID:
PMC1779535
Abstract Full Text PDF–5.8M Supplementary Material

Is Cited by the Following 51 Articles in this Archive:

Robust Analysis of the Yeast Proteome under 50 kDa by Molecular-Mass-Based Fractionation and Top-Down Mass Spectrometry
John F. Kellie, Adam D. Catherman, Kenneth R. Durbin, John C. Tran, Jeremiah D. Tipton, Jeremy L. Norris, Charles E. Witkowski, II, Paul M. Thomas, Neil L. Kelleher
Anal Chem. Author manuscript; available in PMC 2013 January 3.
Published in final edited form as: Anal Chem. 2012 January 3; 84(1): 209–215. Published online 2011 December 14. doi: 10.1021/ac202384v
PMCID:
PMC3262231
Free in PMC on 2013/01/03
System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap
Nagarjuna Nagaraj, Nils Alexander Kulak, Juergen Cox, Nadin Neuhauser, Korbinian Mayr, Ole Hoerning, Ole Vorm, Matthias Mann
Mol Cell Proteomics. 2012 March; 11(3): M111.013722. Published online 2011 October 20. doi: 10.1074/mcp.M111.013722
PMCID:
PMC3316726
Abstract Full Text
Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis
Régis Lavigne, Emmanuelle Becker, Yuchen Liu, Bertrand Evrard, Aurélie Lardenois, Michael Primig, Charles Pineau
Mol Cell Proteomics. 2012 February; 11(2): M111.012682. Published online 2011 October 13. doi: 10.1074/mcp.M111.012682
PMCID:
PMC3277764
Free in PMC on 2013/02/01
Yos9p assists in the degradation of certain nonglycosylated proteins from the endoplasmic reticulum
Laura A. Jaenicke, Holger Brendebach, Matthias Selbach, Christian Hirsch
Mol Biol Cell. 2011 August 15; 22(16): 2937–2945. doi: 10.1091/mbc.E10-10-0832
PMCID:
PMC3154888
Abstract Full Text PDF–851K Supplementary Material
In-depth Quantitative Cardiac Proteomics Combining Electron Transfer Dissociation and the Metalloendopeptidase Lys-N with the SILAC Mouse
Arjen Scholten, Shabaz Mohammed, Teck Y. Low, Sara Zanivan, Toon A. B. van Veen, Bernard Delanghe, Albert J. R. Heck
Mol Cell Proteomics. 2011 October; 10(10): O111.008474. Published online 2011 June 24. doi: 10.1074/mcp.O111.008474
PMCID:
PMC3205878
Free in PMC on 2012/10/01
Widespread RNA and DNA Sequence Differences in the Human Transcriptome
Mingyao Li, Isabel X. Wang, Yun Li, Alan Bruzel, Allison L. Richards, Jonathan M. Toung, Vivian G. Cheung
Science. Author manuscript; available in PMC 2012 January 1.
Published in final edited form as: Science. 2011 July 1; 333(6038): 53–58. Published online 2011 May 19. doi: 10.1126/science.1207018
PMCID:
PMC3204392
Abstract Full Text PDF–428K Supplementary Material
Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments
Genna L. Andrews, Ralph A. Dean, Adam M. Hawkridge, David C. Muddiman
J Am Soc Mass Spectrom. Author manuscript; available in PMC 2012 April 1.
Published in final edited form as: J Am Soc Mass Spectrom. 2011 April; 22(4): 773–783. Published online 2011 February 15. doi: 10.1007/s13361-011-0075-2
PMCID:
PMC3145359
Abstract Full Text PDF–1.1M Supplementary Material
A Robust Method for Quantitative High-throughput Analysis of Proteomes by 18O Labeling
Elena Bonzon-Kulichenko, Daniel Pérez-Hernández, Estefanía Núñez, Pablo Martínez-Acedo, Pedro Navarro, Marco Trevisan-Herraz, María del Carmen Ramos, Saleta Sierra, Sara Martínez-Martínez, Marisol Ruiz-Meana, Elizabeth Miró-Casas, David García-Dorado, Juan Miguel Redondo, Javier S. Burgos, Jesús Vázquez
Mol Cell Proteomics. 2011 January; 10(1): M110.003335. doi: 10.1074/mcp.M110.003335
PMCID:
PMC3013457
Abstract Full Text
Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling
Guoqiang Xu, Jeremy S Paige, Samie R Jaffrey
Nat Biotechnol. Author manuscript; available in PMC 2011 February 1.
Published in final edited form as: Nat Biotechnol. 2010 August; 28(8): 868–873. Published online 2010 July 18. doi: 10.1038/nbt.1654
PMCID:
PMC2946519
Abstract Full Text PDF–1.5M Supplementary Material
Quantitative proteomics: assessing the spectrum of in-gel protein detection methods
Victoria J. Gauci, Elise P. Wright, Jens R. Coorssen
J Chem Biol. 2011 January; 4(1): 3–29. Published online 2010 June 19. doi: 10.1007/s12154-010-0043-5
PMCID:
PMC3022124
Abstract Full Text PDF–456K
Protein and gene model inference based on statistical modeling in k-partite graphs
Sarah Gerster, Ermir Qeli, Christian H. Ahrens, Peter Bühlmann
Proc Natl Acad Sci U S A. 2010 July 6; 107(27): 12101–12106. Published online 2010 June 18. doi: 10.1073/pnas.0907654107
PMCID:
PMC2901486
Abstract Full Text PDF–448K Supplementary Material
Testicular postgenomics: targeting the regulation of spermatogenesis
Pierre Calvel, Antoine D. Rolland, Bernard Jégou, Charles Pineau
Philos Trans R Soc Lond B Biol Sci. 2010 May 27; 365(1546): 1481–1500. doi: 10.1098/rstb.2009.0294
PMCID:
PMC2871924
Abstract Full Text PDF–1.7M
The value of using multiple proteases for large-scale mass spectrometry-based proteomics
Danielle L. Swaney, Craig D. Wenger, Joshua J. Coon
J Proteome Res. Author manuscript; available in PMC 2010 March 5.
Published in final edited form as: J Proteome Res. 2010 March 5; 9(3): 1323–1329. doi: 10.1021/pr900863u
PMCID:
PMC2833215
Abstract Full Text PDF–876K Supplementary Material
Size-Sorting Combined with Improved Nanocapillary-LC-MS for Identification of Intact Proteins up to 80 kDa
Adaikkalam Vellaichamy, John C. Tran, Adam D. Catherman, Ji Eun Lee, John F. Kellie, Steve M.M. Sweet, Leonid Zamdborg, Paul M. Thomas, Dorothy R. Ahlf, Kenneth R. Durbin, Gary A. Valaskovic, Neil L. Kelleher
Anal Chem. Author manuscript; available in PMC 2011 February 15.
Published in final edited form as: Anal Chem. 2010 February 15; 82(4): 1234–1244. doi: 10.1021/ac9021083
PMCID:
PMC2823583
Abstract Full Text PDF–3.1M Supplementary Material
Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography—Tandem Mass Spectrometry
David L. Tabb, Lorenzo Vega-Montoto, Paul A. Rudnick, Asokan Mulayath Variyath, Amy-Joan L. Ham, David M. Bunk, Lisa E. Kilpatrick, Dean D. Billheimer, Ronald K. Blackman, Helene L. Cardasis, Steven A. Carr, Karl R. Clauser, Jacob D. Jaffe, Kevin A. Kowalski, Thomas A. Neubert, Fred E. Regnier, Birgit Schilling, Tony J. Tegeler, Mu Wang, Pei Wang, Jeffrey R. Whiteaker, Lisa J. Zimmerman, Susan J. Fisher, Bradford W. Gibson, Christopher R. Kinsinger, Mehdi Mesri, Henry Rodriguez, Steven E. Stein, Paul Tempst, Amanda G. Paulovich, Daniel C. Liebler, Cliff Spiegelman
J Proteome Res. Author manuscript; available in PMC 2011 February 5.
Published in final edited form as: J Proteome Res. 2010 February 5; 9(2): 761. doi: 10.1021/pr9006365
PMCID:
PMC2818771
Abstract Full Text PDF–2.5M Supplementary Material
Phosphoproteomics by Mass Spectrometry: insights, implications, applications, and limitations
Viveka Mayya, David K. Han
Expert Rev Proteomics. Author manuscript; available in PMC 2010 October 1.
Published in final edited form as: Expert Rev Proteomics. 2009 December; 6(6): 605–618. doi: 10.1586/epr.09.84
PMCID:
PMC2931417
Abstract Full Text PDF–1.9M
Quantitative Proteomics by Metabolic Labeling of Model Organisms
Joost W. Gouw, Jeroen Krijgsveld, Albert J. R. Heck
Mol Cell Proteomics. 2010 January; 9(1): 11–24. Published online 2009 November 19. doi: 10.1074/mcp.R900001-MCP200
PMCID:
PMC2808257
Abstract Full Text
Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance
Amanda G. Paulovich, Dean Billheimer, Amy-Joan L. Ham, Lorenzo Vega-Montoto, Paul A. Rudnick, David L. Tabb, Pei Wang, Ronald K. Blackman, David M. Bunk, Helene L. Cardasis, Karl R. Clauser, Christopher R. Kinsinger, Birgit Schilling, Tony J. Tegeler, Asokan Mulayath Variyath, Mu Wang, Jeffrey R. Whiteaker, Lisa J. Zimmerman, David Fenyo, Steven A. Carr, Susan J. Fisher, Bradford W. Gibson, Mehdi Mesri, Thomas A. Neubert, Fred E. Regnier, Henry Rodriguez, Cliff Spiegelman, Stephen E. Stein, Paul Tempst, Daniel C. Liebler
Mol Cell Proteomics. 2010 February; 9(2): 242–254. Published online 2009 October 26. doi: 10.1074/mcp.M900222-MCP200
PMCID:
PMC2830837
Abstract Full Text Supplementary Material
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Paola Picotti, Bernd Bodenmiller, Lukas N. Mueller, Bruno Domon, Ruedi Aebersold
Cell. Author manuscript; available in PMC 2010 August 21.
Published in final edited form as: Cell. 2009 August 21; 138(4): 795–806. Published online 2009 August 6. doi: 10.1016/j.cell.2009.05.051
PMCID:
PMC2825542
Abstract Full Text PDF–2.6M Supplementary Material
Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics
Cuiping Pan, Jesper V. Olsen, Henrik Daub, Matthias Mann
Mol Cell Proteomics. 2009 December; 8(12): 2796–2808. Published online 2009 August 3. doi: 10.1074/mcp.M900285-MCP200
PMCID:
PMC2816010
Abstract Full Text Supplementary Material
Mining gene functional networks to improve mass-spectrometry-based protein identification
Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. Penalva, Edward M. Marcotte, Daniel P. Miranker
Bioinformatics. 2009 November 15; 25(22): 2955–2961. Published online 2009 July 24. doi: 10.1093/bioinformatics/btp461
PMCID:
PMC2773251
Abstract Full Text PDF–302K
Accurate and Sensitive Peptide Identification with Mascot Percolator
Markus Brosch, Lu Yu, Tim Hubbard, Jyoti Choudhary
J Proteome Res. Author manuscript; available in PMC 2009 August 28.
Published in final edited form as: J Proteome Res. 2009 June; 8(6): 3176–3181. doi: 10.1021/pr800982s
PMCID:
PMC2734080
Abstract Full Text PDF–406K
Analysis of Cell Surface Proteome Changes via Label-free, Quantitative Mass Spectrometry
Ralph Schiess, Lukas N. Mueller, Alexander Schmidt, Markus Mueller, Bernd Wollscheid, Ruedi Aebersold
Mol Cell Proteomics. 2009 April; 8(4): 624–638. doi: 10.1074/mcp.M800172-MCP200
PMCID:
PMC2667347
Abstract Full Text Supplementary Material
Integrating shotgun proteomics and mRNA expression data to improve protein identification
Smriti R. Ramakrishnan, Christine Vogel, John T. Prince, Zhihua Li, Luiz O. Penalva, Margaret Myers, Edward M. Marcotte, Daniel P. Miranker, Rong Wang
Bioinformatics. 2009 June 1; 25(11): 1397–1403. Published online 2009 March 24. doi: 10.1093/bioinformatics/btp168
PMCID:
PMC2682515
Abstract Full Text PDF–270K Supplementary Material
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
Sabine P Schrimpf, Manuel Weiss, Lukas Reiter, Christian H Ahrens, Marko Jovanovic, Johan Malmström, Erich Brunner, Sonali Mohanty, Martin J Lercher, Peter E Hunziker, Ruedi Aebersold, Christian von Mering, Michael O Hengartner
PLoS Biol. 2009 March; 7(3): e1000048. Published online 2009 March 3. doi: 10.1371/journal.pbio.1000048
PMCID:
PMC2650730
Abstract Full Text PDF–649K Supplementary Material
Centrifugal Methods and Devices for Rapid In-Gel Digestion of Proteins
Alexander V. Lazarev, Tomas Rejtar, Shujia Dai, Barry L. Karger
Electrophoresis. Author manuscript; available in PMC 2010 July 20.
Published in final edited form as: Electrophoresis. 2009 March; 30(6): 966–973. doi: 10.1002/elps.200800474
PMCID:
PMC2907145
Abstract Full Text PDF–1.4M Supplementary Material
Auditory proteomics: methods, accomplishments and challenges
Samson Jamesdaniel, Richard Salvi, Donald Coling
Brain Res. Author manuscript; available in PMC 2010 June 24.
Published in final edited form as: Brain Res. 2009 June 24; 1277: 24–36. Published online 2009 February 24. doi: 10.1016/j.brainres.2009.02.026
PMCID:
PMC2764290
Abstract Full Text PDF–921K
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
A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements
Gerhard Mittler, Falk Butter, Matthias Mann
Genome Res. 2009 February; 19(2): 284–293. doi: 10.1101/gr.081711.108
PMCID:
PMC2652210
Abstract Full Text PDF–988K
Lysine 63-linked polyubiquitin chain may serve as a targeting signal for the 26S proteasome
Yasushi Saeki, Tai Kudo, Takayuki Sone, Yoshiko Kikuchi, Hideyoshi Yokosawa, Akio Toh-e, Keiji Tanaka
EMBO J. 2009 February 18; 28(4): 359–371. Published online 2009 January 15. doi: 10.1038/emboj.2008.305
PMCID:
PMC2646160
Abstract Full Text PDF–462K Supplementary Material
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