Subject archive

Proteomics

2009

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

Timo Glatter, Alexander Wepf, Ruedi Aebersold & Matthias Gstaiger

doi:10.1038/msb.2008.75
Published online: 20 January 2009

An atlas of chaperone–protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell

Yunchen Gong, Yoshito Kakihara, Nevan Krogan, Jack Greenblatt, Andrew Emili, Zhaolei Zhang & Walid A Houry

doi:10.1038/msb.2009.26
Published online: 16 June 2009

Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

Esperanza Fernández, Mark O Collins, Rachel T Uren, Maksym V Kopanitsa, Noboru H Komiyama, Mike D R Croning, Lysimachos Zografos, J Douglas Armstrong, Jyoti S Choudhary & Seth G N Grant

doi:10.1038/msb.2009.27
Published online: 19 May 2009

Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology

Brian Cox, Max Kotlyar, Andreas I Evangelou, Vladimir Ignatchenko, Alex Ignatchenko, Kathie Whiteley, Igor Jurisica, S Lee Adamson, Janet Rossant & Thomas Kislinger

doi:10.1038/msb.2009.37
Published online: 16 June 2009

Network-assisted protein identification and data interpretation in shotgun proteomics

Jing Li, Lisa J Zimmerman, Byung-Hoon Park, David L Tabb, Daniel C Liebler & Bing Zhang

doi:10.1038/msb.2009.54
Published online: 18 August 2009

Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes

Li A Kung, Sheng-Ce Tao, Jiang Qian, Michael G Smith, Michael Snyder & Heng Zhu

doi:10.1038/msb.2009.64
Published online: 15 September 2009

2008

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

Arun K Ramani, Zhihua Li, G Traver Hart, Mark W Carlson, Daniel R Boutz & Edward M Marcotte

doi:10.1038/msb.2008.19
Published online: 15 April 2008

Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis

Naoyuki Sugiyama, Hirofumi Nakagami, Keiichi Mochida, Arsalan Daudi, Masaru Tomita, Ken Shirasu & Yasushi Ishihama

doi:10.1038/msb.2008.32
Published online: 06 May 2008

Selected reaction monitoring for quantitative proteomics: a tutorial

Vinzenz Lange, Paola Picotti, Bruno Domon & Ruedi Aebersold

doi:10.1038/msb.2008.61
Published online: 14 October 2008

2007

Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe

Michael W Schmidt, Andres Houseman, Alexander R Ivanov & Dieter A Wolf

doi:10.1038/msb4100117
Published online: 13 February 2007

Large-scale mapping of human protein–protein interactions by mass spectrometry

Rob M Ewing, Peter Chu, Fred Elisma, Hongyan Li, Paul Taylor, Shane Climie, Linda McBroom-Cerajewski, Mark D Robinson, Liam O'Connor, Michael Li, Rod Taylor, Moyez Dharsee, Yuen Ho, Adrian Heilbut, Lynda Moore, Shudong Zhang, Olga Ornatsky, Yury V Bukhman, Martin Ethier, Yinglun Sheng, Julian Vasilescu, Mohamed Abu-Farha, Jean-Philippe Lambert, Henry S Duewel, Ian I Stewart, Bonnie Kuehl, Kelly Hogue, Karen Colwill, Katharine Gladwish, Brenda Muskat, Robert Kinach, Sally-Lin Adams, Michael F Moran, Gregg B Morin, Thodoros Topaloglou & Daniel Figeys

doi:10.1038/msb4100134
Published online: 13 March 2007

Novel peptide identification from tandem mass spectra using ESTs and sequence database compression

Nathan J Edwards

doi:10.1038/msb4100142
Published online: 17 April 2007

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes

Brian Cox, Thomas Kislinger, Dennis A Wigle, Anitha Kannan, Kevin Brown, Tadashi Okubo, Brigid Hogan, Igor Jurisica, Brendan Frey, Janet Rossant & Andrew Emili

doi:10.1038/msb4100151
Published online: 08 May 2007

Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast

Ronish Gupta, Bart Kus, Christopher Fladd, James Wasmuth, Raffi Tonikian, Sachdev Sidhu, Nevan J Krogan, John Parkinson & Daniela Rotin

doi:10.1038/msb4100159
Published online: 05 June 2007

The protein network of bacterial motility

Seesandra V Rajagopala, Björn Titz, Johannes Goll, Jodi R Parrish, Katrin Wohlbold, Matthew T McKevitt, Timothy Palzkill, Hirotada Mori, Russell L Finley, Jr & Peter Uetz

doi:10.1038/msb4100166
Published online: 31 July 2007

PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

Bernd Bodenmiller, Johan Malmstrom, Bertran Gerrits, David Campbell, Henry Lam, Alexander Schmidt, Oliver Rinner, Lukas N Mueller, Paul T Shannon, Patrick G Pedrioli, Christian Panse, Hoo-Keun Lee, Ralph Schlapbach & Ruedi Aebersold

doi:10.1038/msb4100182
Published online: 16 October 2007

2006

Proteome analysis of yeast response to various nutrient limitations

Annemieke Kolkman, Pascale Daran-Lapujade, Asier Fullaondo, Maurien M A Olsthoorn, Jack T Pronk, Monique Slijper & Albert J R Heck

doi:10.1038/msb4100069
Published online: 16 May 2006

An integrated systems approach for understanding cellular responses to gamma radiation

Kenia Whitehead, Adrienne Kish, Min Pan, Amardeep Kaur, David J Reiss, Nichole King, Laura Hohmann, Jocelyne DiRuggiero & Nitin S Baliga

doi:10.1038/msb4100091
Published online: 12 September 2006

Effects of HER2 overexpression on cell signaling networks governing proliferation and migration

Alejandro Wolf-Yadlin, Neil Kumar, Yi Zhang, Sampsa Hautaniemi, Muhammad Zaman, Hyung-Do Kim, Viara Grantcharova, Douglas A Lauffenburger & Forest M White

doi:10.1038/msb4100094
Published online: 03 October 2006

2005

A uniform proteomics MS/MS analysis platform utilizing open XML file formats

Andrew Keller, Jimmy Eng, Ning Zhang, Xiao-jun Li & Ruedi Aebersold

doi:10.1038/msb4100024
Published online: 02 August 2005

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