20 November 2009

Chunxuan Shao, Yuting Liu, Hongqiang Ruan, Ying Li, Haifang Wang, Franziska Kohl, Anna V. Goropashnaya, Vadim B. Fedorov, Rong Zeng, Brian M. Barnes, and Jun Yan

Shotgun proteomic analysis of hibernating arctic ground squirrels
MCP published November 20, 2009, 10.1074/mcp.M900260-MCP200 [Abstract] [Accepted Manuscript]  

19 November 2009

Joost W. Gouw, Jeroen Krijgsveld, and Albert J. R. Heck

Quantitative proteomics by metabolic labeling of model organisms
MCP published November 19, 2009, 10.1074/mcp.R900001-MCP200 [Abstract] [Accepted Manuscript]  

14 November 2009

Izhak Michaelevski, Katalin F Medzihradszky, Aenoch Lynn, Alma L Burlingame, and Mike Fainzilber

Axonal transport proteomics reveals mobilization of translation machinery to the lesion site in injured sciatic nerve
MCP published November 14, 2009, 10.1074/mcp.M900369-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

13 November 2009

Sarah Trimpin, Ellen D. Inutan, Thushani N. Herath, and Charles N. McEwen

Laserspray ionization - A New AP-MALDI Method for Producing Highly Charged Gas-Phase Ions of Peptides and Proteins Directly from Solid Solutions
MCP published November 13, 2009, 10.1074/mcp.M900527-MCP200 [Abstract] [Accepted Manuscript]  

10 November 2009

Marjorie L. Fournier, Ariel Paulson, Norman Pavelka, Amber L. Mosley, Karin Zueckert-Gaudenz, William D. Bradford, Earl Glynn, Hua Li, Mihaela E. Sardiu, Brian Fleharty, Christopher Seidel, Laurence A. Florens, and Michael P. Washburn

Delayed Correlation of mRNA and Protein Expression in Rapamycin Treated Cells and a Role for Ggc1 in Cellular Sensitivity to Rapamycin
MCP published November 10, 2009, 10.1074/mcp.M900415-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Datas]  

Ji Eun Lee, Norman Atkins . Jr, Nathan G. Hatcher, Leonid Zamdborg, Martha U. Gillette, Jonathan V. Sweedler, and Neil L. Kelleher

Endogenous peptide discovery of the rat circadian clock: a focused study of the suprachiasmatic nucleus by ultra-high performance tandem mass spectrometry
MCP published November 10, 2009, 10.1074/mcp.M900362-MCP200 [Abstract] [Accepted Manuscript]  

9 November 2009

Amjad P. Khan, Laila M. Poisson, Vadiraja Bhat, Damian Fermin, Rong Zhao, Shanker Kalyana-Sundaram, George Michailidis, Alexey I. Nesvizhskii, Gilbert S. Omenn, Arul M. Chinnaiyan, and Arun Sreekumar

Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer
MCP published November 9, 2009, 10.1074/mcp.M900159-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

6 November 2009

Feliciano Priego-Capote, Alexander Scherl, Markus Mu¨ller, Patrice Waridel, Frédérique Lisacek, and Jean-Charles Sanchez

Glycation isotopic labelling (GIL) with 13C-reducing sugars for quantitative analysis of glycated proteins in human plasma
MCP published November 6, 2009, 10.1074/mcp.M900439-MCP200 [Abstract] [Accepted Manuscript] [Supplemental DataS]  

2 November 2009

Alexander Y. Andreyev, Zhouxin Shen, Ziqiang Guan, Andrea Ryan, Eoin Fahy, Shankar Subramaniam, Christian R. H. Raetz, Steven Briggs, and Edward A. Dennis

Application of proteomic marker ensembles to subcellular organelle identification
MCP published November 2, 2009, 10.1074/mcp.M900432-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

29 October 2009

Mathieu Baudet, Philippe Ortet, Jean-Charles Gaillard, Bernard Fernandez, Philippe Guérin, Christine Enjalbal, Gilles Subra, Arjan de Groot, Mohamed Barakat, Alain Dedieu, and Jean Armengaud

Proteomic-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons
MCP published October 29, 2009, 10.1074/mcp.M900359-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

Paul A Rudnick, Karl R Clauser, Lisa E Kilpatrick, Dmitrii V Tchekhovskoi, Pedatsur Neta, Niksa Blonder, Dean D Billheimer, Ronald K Blackman, David M Bunk, Helene L Cardasis, Amy-Joan L Ham, Jacob D Jaffe, Christopher R Kinsinger, Mehdi Mesri, Thomas A Neubert, Birgit Schilling, David L Tabb, Tony J Tegeler, Lorenzo Vega-Montoto, Asokan Mulayath Variyath, Mu Wang, Pei Wang, Jeffrey R. Whiteaker, Lisa J. Zimmerman, Steven A. Carr, Susan J. Fisher, Bradford W. Gibson, Amanda G. Paulovich, Fred E. Regnier, Henry Rodriguez, Cliff Spiegelman, Paul Tempst, Daniel C. Liebler, and Stephen E. Stein

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomic analyses and evaluation by the CPTAC network
MCP published October 29, 2009, 10.1074/mcp.M900223-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

28 October 2009

Jacob J. Gano and Julian A. Simon

A proteomic investigation of ligand-dependent HSP90 complexes reveals CHORDC1 as a novel ADP-dependent HSP90 interacting protein
MCP published October 28, 2009, 10.1074/mcp.M900261-MCP200 [Abstract] [Accepted Manuscript]  

27 October 2009

Karl-Johan Leuchowius, Malin Jarvius, Malin Wickström, Linda Rickardson, Ulf Landegren, Rolf Larsson, Ola Söderberg, Mårten Fryknäs, and Jonas Jarvius

High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation
MCP published October 27, 2009, 10.1074/mcp.M900331-MCP200 [Abstract] [Accepted Manuscript]  

26 October 2009

Amanda G. Paulovich, Dean Billheimer, Amy-Joan L. Ham, Lorenzo Jorge 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. Reginier, Henry Rodriguez, Cliff Spiegelman, Stephen E. Stein, Paul Tempst, and Daniel C. Liebler

A CPTAC inter-laboratory study characterizing a yeast performance standard for benchmarking LC-MS Platform performance
MCP published October 26, 2009, 10.1074/mcp.M900222-MCP200 [Abstract] [Accepted Manuscript]  

20 October 2009

Meng-Hsuan Han, Chengyi Lin, Shuxia Meng, and Xiaozhong Wang

Proteomic analysis reveals overlapping functions of clustered protocadherins
MCP published October 20, 2009, 10.1074/mcp.M900343-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

Jeffrey R. Whiteaker, Lei Zhao, Leigh Anderson, and Amanda G. Paulovich

An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers
MCP published October 20, 2009, 10.1074/mcp.M900254-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

16 October 2009

Suresh Mathivanan, Justin W. E. Lim, Bow J. Tauro, Hong Ji, Roberts L. Moritz, and Richard J. Simpson

Proteomic analysis of A33-immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature
MCP published October 16, 2009, 10.1074/mcp.M900152-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

14 October 2009

Jesper V Olsen, Jae C Schwartz, Jens Griep-Raming, Michael L Nielsen, Eugen Damoc, Eduard Denisov, Oliver Lange, Philip Remes, Dennis Taylor, Maurizio Splendore, Eloy R Wouters, Michael Senko, Alexander Makarov, Matthias Mann, and Stevan Horning

A dual pressure linear ion trap - Orbitrap instrument with very high sequencing speed
MCP published October 14, 2009, 10.1074/mcp.M900375-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

7 October 2009

Bai-Yu Lee, Deepa Jethwaney, Birgit Schilling, Daniel L. Clemens, Bradford W. Gibson, and Marcus A. Horwitz

The mycobacterium bovis BCG phagosome proteome
MCP published October 7, 2009, 10.1074/mcp.M900396-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

Yun W. Lam, Vanessa C. Evans, Kate J. Heesom, Angus I. Lamond, and David A. Matthews

Proteomic analysis of the nucleolus in adenovirus-infected cells
MCP published October 7, 2009, 10.1074/mcp.M900338-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

6 October 2009

Feixia Chu, Peter R. Baker, A L. Burlingame, and Robert J. Chalkley

Finding Chimeras: A bioinformatic strategy for identification of cross-linked peptides
MCP published October 6, 2009, 10.1074/mcp.M800555-MCP200 [Abstract] [Accepted Manuscript]  

5 October 2009

Pai-Chiao Cheng, Hsiang-Kai Chang, and Shu-Hui Chen

Quantitative nano-proteomics for protein complexes (QNanoPX) related to estrogen transcriptional action
MCP published October 5, 2009, 10.1074/mcp.M900183-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

2 October 2009

Wei Yang, Dolores Di Vizio, Marc Kirchner, Hanno Steen, and Michael R. Freeman

Proteome-scale characterization of human s-acylated proteins in lipid raft-enriched and non-raft membranes
MCP published October 2, 2009, 10.1074/mcp.M800448-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

28 September 2009

Nurhan Ozlu, Flavio Monigatti, Bernhard Y. Renard, Christine M. Field, Hanno Steen, Timothy J. Mitchison, and Judith J. Steen

Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition
MCP published September 28, 2009, 10.1074/mcp.M900308-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

Marko Radulovic, Eleanor Crane, Mark Crawford, Jasminka Godovac Zimmermann, and Veronica P. C. C. Yu

Cks proteins protect mitochondrial genome integrity by interacting with mitochondrial single-stranded DNA binding protein
MCP published September 28, 2009, 10.1074/mcp.M900078-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

25 September 2009

Jose M. Moreira, Gita Ohlsson, Pavel Gromov, Ronald Simon, Guido Sauter, Julio E. Celis, and Irina Gromova

Bladder cancer associated protein: a potential prognostic biomarker in human bladder cancer
MCP published September 25, 2009, 10.1074/mcp.M900294-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

23 September 2009

Chris Planque, Vathany Kulasingan, Chris R. Smith, Karen Reckamp, Lee Goodglick, and Eleftherios P. Diamandis

Identification of five candidate lung cancer biomarkers by proteomic analysis of conditioned media of four lung cancer cell lines
MCP published September 23, 2009, 10.1074/mcp.M900134-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

21 September 2009

Paul J Boersema, Leong Yan Foong, Vanessa M.Y. Ding, Simone Lemeer, Bas van Breukelen, Robin Philp, Jos Boekhorst, Berend Snel, Jeroen den Hertog, Andre B.H. Choo, and Albert J. R. Heck

In depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immuno-affinity purification and stable isotope dimethyl labeling
MCP published September 21, 2009, 10.1074/mcp.M900291-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

18 September 2009

Takeshi Masuda, Natsumi Saito, Masaru Tomita, and Yasushi Ishihama

Unbiased quantitation of Escherichia coli membrane proteome using phase-transfer surfactants
MCP published September 18, 2009, 10.1074/mcp.M900240-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

16 September 2009

Dieter Demon, Petra Van Damme, Tom Vanden Berghe, Annelies Deceuninck, Joost Van Durme, Jelle Verspurten, Kenny Helsens, Francis Impens, Magdalena Wejda, Joost Schymkowitz, Frederic Rousseau, Annemieke Madder, Joël Vandekerckhove, Wim Declercq, Kris Gevaert, and Peter Vandenabeele

Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity
MCP published September 16, 2009, 10.1074/mcp.M900310-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

15 September 2009

Stuart A. Cain, Amanda McGovern, Elaine Small, Lyle J. Ward, Clair Baldock, Adrian Shuttleworth, and Cay M. Kielty

Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach
MCP published September 15, 2009, 10.1074/mcp.M900008-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

14 September 2009

Rudolf Lichtenfels, Sven P Dressler, Monica Zobawa, Christian V Recktenwald, Angelika Ackermann, Derek Atkins, Michael Kersten, Andrea Hesse, Maria Puttkammer, Friedrich Lottspeich, and Barbara Seliger

Systematic comparative protein expression profiling of clear cell renal cell carcinoma: A pilot study based on the separation of tissue specimen by two-dimensional electrophoresis
MCP published September 14, 2009, 10.1074/mcp.M900168-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

13 September 2009

Chih-Chiang Tsou, Chia-Feng Tasi, Ying-Hao Tsui, Putty-Reddy Sudhir, Yi-Ting Wang, Yu-Ju Chen, Jeou-Yuan Chen, Ting-Yi Sung, and Wen-Lian Hsu

IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation
MCP published September 13, 2009, 10.1074/mcp.M900177-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

9 September 2009

Bart Ghesquière, Niklaas Colaert, Kenny Helsens, Lien Dejager, Caroline Vanhaute, Katleen Verleysen, Koen Kas, Evy Timmerman, Marc Goethals, Claude Libert, Joël Vandekerckhove, and Kris Gevaert

In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography
MCP published September 9, 2009, 10.1074/mcp.M900259-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

Yan Luo, Christian Blex, Olivia Baessler, Mirko Glinski, Mathias Dreger, Michael Sefkow, and Hubert Köster

From PKA to HCN: The cAMP-capture compound mass spectrometry as a novel tool for targeting cAMP binding proteins
MCP published September 9, 2009, 10.1074/mcp.M900110-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

3 September 2009

Zhenying Peng, Mengcheng Wang, Fei Li, Hongjun Lv, Cuiling Li, and Guangmin Xia

A proteomic study of the response to salinity and drought stress in an introgression strain of bread wheat
MCP published September 3, 2009, 10.1074/mcp.M900052-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

1 September 2009

Nadia Rachdaoui, Leanne Austin, Eric Kramer, Michael J. Previs, Vernon E. Anderson, Takhar Kasumov, and Stephen F. Previs

Measuring proteome dynamics in vivo: As easy as adding water?
MCP published September 1, 2009, 10.1074/mcp.M900026-MCP200 [Abstract] [Accepted Manuscript]  

31 August 2009

Sebastien Jacquet, Xiaoke Yin, Pierre Sicard, James Clark, Gajen S. Skanaganayagam, Manuel Mayr, and Michael S. Marber

Identification of cardiac myosin binding protein C as a candidate biomarker of myocardial infarction by proteomic analysis
MCP published August 31, 2009, 10.1074/mcp.M900176-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data] [Supplemental Data]  

He-Hsuan Hsiao, Erik Meulmeester, Benedikt T. C. Frank, Frauke Melchior, and Henning Urlaub

“ChopNspice”, a mass-spectrometric approach that allows identification of endogenous SUMO-conjugated peptides
MCP published August 31, 2009, 10.1074/mcp.M900087-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

23 August 2009

Wen-Jun Deng, Song Nie, JIe Dai, Jia-Rui Wu, and Rong Zeng

Proteome, phosphoproteome and hydroxyproteome of liver mitochondria in diabetic rats at early pathogenic stages
MCP published August 23, 2009, 10.1074/mcp.M900020-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

20 August 2009

Miao-Hsia Lin, Tung-Li Hsu, Shu-Yu Lin, Yi-Jiun Pan, Jia-Tsrong Jan, Jin-Town Wang, Kay-Hooi Khoo, and Shih-Hsiung Wu

Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence
MCP published August 20, 2009, 10.1074/mcp.M900276-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

19 August 2009

Zihao Wang, Namrata D. Udeshi, Meaghan O'Malley, Jeffrey Shabanowitz, Donald F. Hunt, and Gerald W. Hart

Enrichment and site-mapping of O-Linked N-Acetylglucosamine by a combination of chemical/enzymatic tagging, photochemical cleavage, and electron transfer dissociation (ETD) mass spectrometry
MCP published August 19, 2009, 10.1074/mcp.M900268-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

12 August 2009

Yi-Bo Wu, Jie Dai, Xing-Lin Yang, Su-Jun Li, Shi-Lin Zhao, Jia-Shu Tang, Guang-Yong Zheng, Yi-Xue Li, Jia-Rui Wu, and Rong Zeng

Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression
MCP published August 12, 2009, 10.1074/mcp.M900293-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

11 August 2009

Amanda L. Klein, Mary N. Berkaw, Maria G. Buse, and Lauren E. Ball

O-GlcNAc modification of insulin receptor substrate-1 (IRS-1) occurs in close proximity to multiple SH2 domain binding motifs
MCP published August 11, 2009, 10.1074/mcp.M900207-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

David E. Gloriam, Sandra Orchard, Daniela Bertinetti, Erik Bjorling, Erik Bongcam-Rudloff, Julie Bourbeillon, Andrew R. Bradbury, Antoine de Daruvar, Stefan Dubel, Roanld Frank, Toby J. Gibson, Niall Haslam, Friedrich W. Herberg, Tara Hiltke, Jorg D. Hoheisel, Samuel Kerrien, Manfred Koegl, Zoltan Konthur, Bernhard Korn, Ulf Landegren, Silvere van der Maarel, Luisa Montecchi-Palazzi, Sandrine Palcy, Henry Rodriguez, Sonja Schweinsberg, Volker Sievert, Oda Stoevesandt, Michael J. Taussig, Mathias Uhlen, Christer Wingren, Larry Gold, Peter Woollard, David J. Sherman, and Hennig Hermjakob

Report: A community standard format for the representation of protein affinity reagents
MCP published August 11, 2009, 10.1074/mcp.M900185-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

3 August 2009

Cuiping Pan, Jesper V. Olsen, Henrik Daub, and Matthias Mann

Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics
MCP published August 3, 2009, 10.1074/mcp.M900285-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

29 July 2009

Tobias Reinl, Manfred Nimtz, Claudia Hundertmark, Thorsten Johl, György Kéri, Jürgen Wehland, Henrik Daub, and Lothar Jänsch

Quantitative phosphokinome analysis of the Met pathway activated by the invasin InlB from listeria monocytogenes
MCP published July 29, 2009, 10.1074/mcp.M800521-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

17 July 2009

Katherine A. Ewen, Mark A. Baker, Dagmar Wilhelm, R John Aitken, and Peter A. Koopman

Global survey of protein expression during gonadal sex determination in mice
MCP published July 17, 2009, 10.1074/mcp.M900108-MCP200 [Abstract] [Accepted Manuscript] [Supplemental Data]  

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