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Ruedi Aebersold

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Matthias Gstaiger; Ruedi Aebersold
Genotype-phenotype relationships in light of a modular protein interaction landscape.
Olga T Schubert; Zhi Sun; Patrick K Arthur; David S Campbell; Manfred Claassen; Terry Farrah; Martin Gengenbacher; Stefan H E Kaufmann; Christina Ludwig; Alessio Maiolica; Robert L Moritz; Jeppe Mouritsen; George Rosenberger; Hannes L Röst; Ruedi Aebersold
The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis.
Markku Varjosalo; Anton Vichalkovski; Ruedi Aebersold; Salla Keskitalo; Helka Nurkkala; Audrey Van Drogen; Matthias Gstaiger
The Protein Interaction Landscape of the Human CMGC Kinase Group.

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All Publications

2013: Matthias Gstaiger; Ruedi Aebersold
Genotype-phenotype relationships in light of a modular protein interaction landscape.
Molecular bioSystems 2013;9(6):1064-7.
2013: Olga T Schubert; Zhi Sun; Patrick K Arthur; David S Campbell; Manfred Claassen; Terry Farrah; Martin Gengenbacher; Stefan H E Kaufmann; Christina Ludwig; Alessio Maiolica; Robert L Moritz; Jeppe Mouritsen; George Rosenberger; Hannes L Röst; Ruedi Aebersold
The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis.
Cell host & microbe 2013;13(5):602-12.
2013: Markku Varjosalo; Anton Vichalkovski; Ruedi Aebersold; Salla Keskitalo; Helka Nurkkala; Audrey Van Drogen; Matthias Gstaiger
The Protein Interaction Landscape of the Human CMGC Kinase Group.
Cell reports 2013;3(4):1306-20.
2013: Ina Stützer; Ruedi Aebersold; Daria Esterházy; Alexander Schmidt; Nathalie Selevsek; Markus Stoffel
Systematic proteomic analysis identifies β-site amyloid precursor protein cleaving enzyme 2 and 1 (BACE2 and BACE1) substrates in pancreatic β-cells.
The Journal of biological chemistry 2013;288(15):10536-47.
2013: Markku Varjosalo; Audrey van Drogen; Ruedi Aebersold; Keiryn L Bennett; Jacques Colinge; Matthias Gstaiger; Simon Hauri; Melanie Planyavsky; Roberto Sacco; Alexey Stukalov; Giulio Superti-Furga
Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS.
Nature methods 2013;10(4):307-14.
2013: Ruth Hüttenhain; Ulrike Kusebauch; Robert L Moritz; Reto Ossola; Oliver Rinner; George Rosenberger; Ralph Schiess; Zhi Sun; Silvia Surinova; Bernd Wollscheid; Damaris Bausch-Fluck; David Campbell; Ferdinando Cerciello; Jingchung Chen; Marián Hajdúch; Ruedi Aebersold
N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications.
Molecular & cellular proteomics : MCP 2013;12(4):1005-16.
2013: Yansheng Liu; Jeppe Mouritsen; Pedro Navarro; Silvia Surinova; Roland Brunner; Ludovic C J Gillet; Ruth Hüttenhain; Ruedi Aebersold
Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS.
Proteomics 2013;13(8):1247-56.
2013: Ferdinand von Meyenn; Ruedi Aebersold; Emanuel Gasser; Thomas Porstmann; Alexander Schmidt; Nathalie Selevsek; Markus Stoffel
Glucagon-induced acetylation of Foxa2 regulates hepatic lipid metabolism.
Cell metabolism 2013;17(3):436-47.
2013: Matteo Berti; Valentina Biasin; Arnab Ray Chaudhuri; Timo Glatter; Shivasankari Gomathinayagam; Simona Graziano; Matthias Gstaiger; Sasa Kenig; Massimo Lopes; Bojana Lucic; Francesca Marino; Ramiro Mendoza-Maldonado; Raymond J Monnat; Federico Odreman; Julia M Sidorova; Saravanabhavan Thangavel; Ruedi Aebersold; Marko Vujanovic; Alessandro Vindigni
Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition.
Nature structural & molecular biology 2013;20(3):347-54.
2013: Hamid Mirzaei; Paola Picotti; Max Robinson; Ilya Shmulevich; Ruedi Aebersold; John D Aitchison; Gregory Carter; David J Dilworth; Jimmy K Eng; Timothy Galitski; Bong Kim; Theo A Knijnenburg; Song Li; Jeffrey A Ranish
Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(9):3645-50.
2013: Frank Wippich; Ruedi Aebersold; Bernd Bodenmiller; Maria Gustafsson Trajkovska; Stefanie Wanka; Lucas Pelkmans
Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling.
Cell 2013;152(4):791-805.
2013: Paola Picotti; Lukas Reiter; Oliver Rinner; Hannes Röst; Alexander Schmidt; Qin Shen; Zhi Sun; Bernd Wollscheid; Simon Alberti; Andreas Beyer; David S Campbell; Mathieu Clément-Ziza; Eric Deutsch; Andreas Frei; Ulrike Kusebauch; Henry Lam; Jacob J Michaelson; Robert L Moritz; Ruedi Aebersold
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis.
Nature 2013;494(7436):266-70.
2013: Catherine C L Wong; Ruedi Aebersold; Daniel Cociorva; Christine A Miller; Craig Monell; Alexander Schmidt; John R Yates
Proteomics of Pyrococcus furiosus (Pfu): Identification of Extracted Proteins by Three Independent Methods.
Journal of proteome research 2013;12(2):763-70.
2013: Séverine Bontron; Ruedi Aebersold; Bernd Bodenmiller; Malika Jaquenoud; Nicolas Talarek; Stefania Vaga; Claudio de Virgilio
Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A.
Cell reports 2013;3(1):16-22.
2013: Ruedi Aebersold; Gary D Bader; Aled M Edwards; Martin Kussmann; Jun Qin; Jennifer E Van Eyk; Gilbert S Omenn
The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community.
Journal of proteome research 2013;12(1):23-7.
2013: Guillermo G Zampar; Ruedi Aebersold; Jennifer Ewald; Stefan Jol; Anne Kümmel; Bastian Niebel; Paola Picotti; Uwe Sauer; Nicola Zamboni; Matthias Heinemann
Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.
Molecular systems biology 2013;9():651.
2013: Paola Picotti; Bernd Bodenmiller; Ruedi Aebersold
Proteomics meets the scientific method.
Nature methods 2013;10(1):24-7.
2012: Chih-Chien Wu; Ruedi Aebersold; Patrick Cramer; Franz Herzog; Stefan Jennebach; Yu-Chun Lin; Chih-Yu Pai; Hung-Ta Chen
RNA polymerase III subunit architecture and implications for open promoter complex formation.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(47):19232-7.
2012: Timo Glatter; Albert J R Heck; Christina Ludwig; Ruedi Aebersold; Erik Ahrné; Alexander Schmidt
Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion.
Journal of proteome research 2012;11(11):5145-56.
2012: Samuel Marguerat; Alexander Schmidt; Ruedi Aebersold; Wei Chen; Sandra Codlin; Jürg Bähler
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Cell 2012;151(3):671-83.
2012: Thomas Bock; Silvia Dolski; Andreas Frei; Karl Frei; Andreas Hofmann; Andrea Jacobs; Niklaus Krayenbuehl; Emma Lundberg; Hansjoerg Moest; Ulrich Omasits; Mathias Uhlen; Ruedi Aebersold; Damaris Bausch-Fluck; Bernd Wollscheid
Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.
Journal of proteome research 2012;11(10):4885-93.
2012: Andreas P Frei; Lisa M Henning; Ock-Youm Jeon; Christian Jost; Samuel Kilcher; Jason Mercer; Hansjoerg Moest; Andreas Plückthun; Ruedi Aebersold; Erick M Carreira; Bernd Wollscheid
Direct identification of ligand-receptor interactions on living cells and tissues.
Nature biotechnology 2012;30(10):997-1001.
2012: Ko Sato; Ralph Schiess; Anna S Sedukhina; Elayanambi Sundaramoorthy ; Ruedi Aebersold; Nabieh Ayoub; Hiroyoshi Hattori; Anand D Jeyasekharan; Hiroyuki Nishikawa; Tomohiko Ohta; Eeson Rajendra; Haruka Wada; Ashok R Venkitaraman
A DNA-damage selective role for BRCA1 E3 ligase in claspin ubiquitylation, CHK1 activation, and DNA repair.
Current biology : CB 2012;22(18):1659-66.
2012: Franz Herzog; Abdullah Kahraman; Alexander Leitner; Raymond Mak; Lars Malmström; Thomas Walzthoeni; Nenad Ban; Martin Beck; Daniel Boehringer; Andreas Bracher; Franz-Ulrich Hartl; Ruedi Aebersold
Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry.
Science (New York, N.Y.) 2012;337(6100):1348-52.
2012: Stine L Bislev; Ruedi Aebersold; Emøke Bendixen; Eric Deutsch; Terry Farrah; Robert L Moritz; Zhi Sun; Marius C Codrea
A Bovine PeptideAtlas of milk and mammary gland proteomes.
Proteomics 2012;12(18):2895-9.
2012: Leroy E Hood; Jennie Hunter-Cevera; Laurie Locascio; Robert L Moritz; Gilbert S Omenn; Keith R Yamamoto; Ruedi Aebersold; Michael Amos
New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences.
Proteomics 2012;12(18):2773-83.
2012: Thomas Walzthoeni; Martin Beck; Stefan Bohn; Manfred Claassen; Friedrich Förster; Franz Herzog; Alexander Leitner; Ruedi Aebersold
False discovery rate estimation for cross-linked peptides identified by mass spectrometry.
Nature methods 2012;9(9):901-3.
2012: Bernhard M Kohli; Ruedi Aebersold; Giovanni Carbonetti; Lukas N Mueller; Roger M Nitsch; Delphine Pflieger; Uwe Konietzko
Interactome of the amyloid precursor protein APP in brain reveals a protein network involved in synaptic vesicle turnover and a close association with Synaptotagmin-1.
Journal of proteome research 2012;11(8):4075-90.
2012: Hannes Röst; Lars Malmström; Ruedi Aebersold
A computational tool to detect and avoid redundancy in selected reaction monitoring.
Molecular & cellular proteomics : MCP 2012;11(8):540-9.
2012: Eduard Sabidó; Nathalie Selevsek; Ruedi Aebersold
Mass spectrometry-based proteomics for systems biology.
Current opinion in biotechnology 2012;23(4):591-7.
2012: Ruth Hüttenhain; Ulrike Kusebauch; Robert L Moritz; Emma Niméus-Malmström; Oliver Rinner; Hannes Röst; Nathalie Selevsek; Atul Sethi; Martin Soste; Christine Carapito; Eric Deutsch; Terry Farrah; Ruedi Aebersold
Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics.
Science translational medicine 2012;4(142):142ra94.
2012: Marko Jovanovic; Ethan Kaufman; Eric A Miska; Lukas J Neukomm; Paola Picotti; Hubert Rehrauer; Lukas Reiter; Martin J Simard; Manuel Weiss; Bernd Wollscheid; Ruedi Aebersold; Alejandra Clark; Andreas Frei; André P Gerber; Michael O Hengartner
RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans.
Genome research 2012;22(7):1360-71.
2012: Stefan Jennebach; Franz Herzog; Ruedi Aebersold; Patrick Cramer
Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage.
Nucleic acids research 2012;40(12):5591-601.
2012: Eduard Sabidó; Ishita Shah; Qin Shen; Olga Vitek; Alexander Andreyev; Aaron M Armando; Ching-Yun Chang; Edward A Dennis; Oswald Quehenberger; Ruedi Aebersold
Targeted proteomics of the eicosanoid biosynthetic pathway completes an integrated genomics-proteomics-metabolomics picture of cellular metabolism.
Molecular & cellular proteomics : MCP 2012;11(7):M111.014746.
2012: Alessio Maiolica; Iakes Ezkurdia; Martin A Jünger; Ruedi Aebersold
Targeted proteome investigation via selected reaction monitoring mass spectrometry.
Journal of proteomics 2012;75(12):3495-513.
2012: Arto T Pulliainen; Maxime Quebatte; Alexander Wepf; Ruedi Aebersold; Alex Böhm; Cameron S Brand; Carmen W Dessauer; Matthias Gstaiger; Barbara Hauert; Kathrin Pieles; Christoph Dehio
Bacterial effector binds host cell adenylyl cyclase to potentiate Gαs-dependent cAMP production.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(24):9581-6.
2012: Paola Picotti; Ruedi Aebersold
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions.
Nature methods 2012;9(6):555-66.
2012: Ludovic C Gillet; Pedro Navarro; Lukas Reiter; Hannes Röst; Nathalie Selevsek; Stephen Tate; Ron Bonner; Ruedi Aebersold
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.
Molecular & cellular proteomics : MCP 2012;11(6):O111.016717.
2012: Alexander Leitner; Steve Ludtke; Boxue Ma; Leonie Mönkemeyer; Sebastian Pechmann; Thomas Walzthoeni; Ruedi Aebersold; Andreas Bracher; Bryan Chen; Wah Chiu; Yao Cong; F Ulrich Hartl; Susan Holmes; Lukasz A Joachimiak; Judith Frydman
The molecular architecture of the eukaryotic chaperonin TRiC/CCT.
Structure (London, England : 1993) 2012;20(5):814-25.
2012: Sofia Waldemarson; Ruedi Aebersold; Ayodele A Alaiya; Gert Auer; Karin M Hansson; Ufuk Kirik; Morten Krogh; Hookeun Lee; Johan Malmström; Reto Ossola; Kjell Schedvins; Peter James
Protein expression changes in ovarian cancer during the transition from benign to malignant.
Journal of proteome research 2012;11(5):2876-89.
2012: Young-Ki Paik; Ghasem Hosseini Salekdeh; Mathias Uhlen; Tadashi Yamamoto; Jong Shin Yoo; Ruedi Aebersold; Alexander Archakov; Amos Bairoch; Mark S Baker; John Bergeron; Pierre-Alain Binz; Jerome Garin; Samir Hanash; Fuchu He; Seul-Ki Jeong; Paul Keown; Hyoung-Joo Lee; Pierre Legrain; György Marko-Varga; Keun Na; Toshihide Nishimura; Gilbert S Omenn; William S Hancock
Standard guidelines for the chromosome-centric human proteome project.
Journal of proteome research 2012;11(4):2005-13.
2012: H Alexander Ebhardt; Ruth Hüttenhain; Eduard Sabidó; Ben Collins; Ruedi Aebersold
Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate.
Proteomics 2012;12(8):1185-93.
2012: Christine Carapito; Ruedi Aebersold
Targeted proteomics.
Proteomics 2012;12(8):1073.
2012: Terry Farrah; Ruth Hüttenhain; Richard Kreisberg; Ulrike Kusebauch; Luis Mendoza; Ruedi Aebersold; Mi-Youn Brusniak; David S Campbell; Eric Deutsch; Ralph Schiess; Nathalie Selevsek; Zhi Sun; Robert L Moritz
PASSEL: the PeptideAtlas SRMexperiment library.
Proteomics 2012;12(8):1170-5.
2012: Ching-Yun Chang; Viola Heinzelmann-Schwarz; Ruth Hüttenhain; Marko Jovanovic; Paola Picotti; Ruedi Aebersold; Olga Vitek
Protein significance analysis in selected reaction monitoring (SRM) measurements.
Molecular & cellular proteomics : MCP 2012;11(4):M111.014662.
2012: Eric Deutsch; Kenny Helsens; Fredrik Levander; Lennart Martens; Luis Mendoza; Robert L Moritz; Steffen Neumann; David Ovelleiro; Jim Shofstahl; Ruedi Aebersold; Pierre-Alain Binz; David S Campbell; Matthew Chambers; Mi-Youn Brusniak
TraML--a standard format for exchange of selected reaction monitoring transition lists.
Molecular & cellular proteomics : MCP 2012;11(4):R111.015040.
2012: Manfred Claassen; Michael O Hengartner; Lukas Reiter; Joachim M Buhmann; Ruedi Aebersold
Generic comparison of protein inference engines.
Molecular & cellular proteomics : MCP 2012;11(4):O110.007088.
2012: Lars Malmström; George Rosenberger; Nathalie Selevsek; Johan Malmström; Ruedi Aebersold
Automated workflow for large-scale selected reaction monitoring experiments.
Journal of proteome research 2012;11(3):1644-53.
2012: Stine L Bislev; Marius C Codrea; Victoria M Harman; Ulrike Kusebauch; Robert L Moritz; Christine M Røntved; Ruedi Aebersold; Robert J Beynon; Emøke Bendixen
Quantotypic properties of QconCAT peptides targeting bovine host response to Streptococcus uberis.
Journal of proteome research 2012;11(3):1832-43.
2012: Young-Ki Paik; Michael Snyder; Allen D Taylor; Mathias Uhlen; Fangfei Yan; Fan Zhang; Yue Zhang; Ruedi Aebersold; Amos Bairoch; Rui Chen; Yong Cheng; Sang Yun Cho; Eun-Young Choi; Eric W Deutsch; Samir Hanash; Denis Hochstrasser; Seul-Ki Jeong; Hoguen Kim; Kwang Youl Kim; Ja-Young Kwon; Eun-Young Lee; Hyoung-Joo Lee; Pierre Legrain; György Marko-Varga; Keun Na; Gilbert S Omenn; William S Hancock
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.
Nature biotechnology 2012;30(3):221-3.
2012: Angus I Lamond; Michal Linial; Alexander Makarov; Ruedi Aebersold; Jens S Andersen; Wolfgang Baumeister; F Ulrich Hartl; Stevan Horning; Carol V Robinson; Luis Serrano; Mathias Uhlen; Ole Vorm; anne katrin werenskiold; Matthias Mann
Advancing cell biology through proteomics in space and time (PROSPECTS).
Molecular & cellular proteomics : MCP 2012;11(3):O112.017731.
2012: Alexander Leitner; Roland Reischl; Thomas Walzthoeni; Stefan Bohn; Friedrich Förster; Franz Herzog; Ruedi Aebersold
Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography.
Molecular & cellular proteomics : MCP 2012;11(3):M111.014126.
2012: Florian Stengel; Ruedi Aebersold; Carol V Robinson
Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes.
Molecular & cellular proteomics : MCP 2012;11(3):R111.014027.
2012: Christina Ludwig; Alexander Schmidt; Manfred Claassen; Ruedi Aebersold
Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry.
Molecular & cellular proteomics : MCP 2012;11(3):M111.013987.
2012: Alexandra M E Jones; Marko Jovanovic; Craig Lawless; Günter Lochnit; Lennart Martens; Christian Ravnsborg; Sabine P Schrimpf; Yhong-Hee Shim; Deni Subasic; Andreas Tholey; Manuel Weiss; Ruedi Aebersold; Christian H Ahrens; Rolf Apweiler; Katja Baerenfaller; Mark Baker; Emøke Bendixen; Steve Briggs; Philip Brownridge; Erich Brunner; Michael Daube; Eric Deutsch; Ueli Grossniklaus; Joshua L Heazlewood; Michael O Hengartner; Henning Hermjakob; Christian von Mering; Klaas van Wijk; Xue Zheng
The HUPO initiative on Model Organism Proteomes, iMOP.
Proteomics 2012;12(3):340-5.
2012: Keren Lasker; Andrej Sali; Pia Unverdorben; Elizabeth Villa; Thomas Walzthoeni; Ruedi Aebersold; Florian Beck; Stefan Bohn; Friedrich Förster; Wolfgang Baumeister
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(5):1380-7.
2012: Christofer Karlsson; Ruedi Aebersold; Lars Malmström; Johan Malmström
Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes.
Nature communications 2012;3():1301.
2012: Timothy Clough; Susanne Ragg; Safia Thaminy; Ruedi Aebersold; Olga Vitek
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs.
BMC bioinformatics 2012;13 Suppl 16():S6.
2012: Ana Paula Oliveira; Paola Picotti; Ruedi Aebersold; Maria Kogadeeva; Christina Ludwig; Uwe Sauer
Regulation of yeast central metabolism by enzyme phosphorylation.
Molecular systems biology 2012;8():623.
2012: Claudio Ciferri; Franz Herzog; Gabriel C Lander; Alessio Maiolica; Ruedi Aebersold; Eva Nogales
Molecular architecture of human polycomb repressive complex 2.
eLife 2012;1():e00005.
2012: Ariel Bensimon; Albert J R Heck; Ruedi Aebersold
Mass spectrometry-based proteomics and network biology.
Annual review of biochemistry 2012;81():379-405.
2011: Roger Higdon; Ruedi Aebersold; Andrew T Bauman; Gregory Hather; Winston Haynes; Natali Kolker; Paola Picotti; Lukas Reiter; Alexander Schmidt; Elizabeth Stewart; Gerald van Belle; Eugene Kolker
IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
Journal of proteomics 2011;75(1):116-21.
2011: David Shteynberg; Zhi Sun; Natalie Tasman; Ruedi Aebersold; Eric Deutsch; Jimmy K Eng; Henry Lam; Luis Mendoza; Robert L Moritz; Alexey I Nesvizhskii
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.
Molecular & cellular proteomics : MCP 2011;10(12):M111.007690.
2011: Martin Kälin; Wilhelm Krek; Tom Powles; Ralph Schiess; Arnoud Templeton; Peter Wild; Ruedi Aebersold; Thomas Cerny; Igor Cima; Niklaus Fankhauser; Silke Gillessen
Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome.
European urology 2011;60(6):1235-43.
2011: Ruedi Aebersold
Editorial: from data to results.
Molecular & cellular proteomics : MCP 2011;10(11):E111.014787.
2011: Claudia Blattner; Alan C M Cheung; Ruedi Aebersold; Albert J R Heck; Franz Herzog; Karl-Peter Hopfner; Stefan Jennebach; Kristina Lorenzen; Andreas Mayer; Gregor Witte; Patrick Cramer
Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth.
Genes & development 2011;25(19):2093-105.
2011: Seok-Won Hyung; Hee-Jung Jung; Kyung-Min Lee; Min Young Lee; Sang-Won Lee; Hyeong-Gon Moon; Jong-Moon Park; Byunghee Shin; Jong-Han Yu; Myeong-Hee Yu; HUI ZHANG; Ruedi Aebersold; Wonshik Han; Daehee Hwang; Dong-Young Noh
A serum protein profile predictive of the resistance to neoadjuvant chemotherapy in advanced breast cancers.
Molecular & cellular proteomics : MCP 2011;10(10):M111.011023.
2011: Andrew N Hoofnagle; Ruedi Aebersold; N Leigh Anderson; Adam Felsenfeld; Daniel C Liebler
Painting a moving picture: large-scale proteomics efforts and their potential for changing patient care.
Clinical chemistry 2011;57(10):1357-60.
2011: Daria Esterházy; Hans Hilpert; Julie Kerr Conte; Nora Lieske; Lorella Marselli; Hugues Matile; Cristiano Migliorini; Holger Moch; Michael Prummer; Markus P Rechsteiner; Alexander Schmidt; Giatgen Andreia Spinas; Ruedi Aebersold; Jeremy Beauchamp; Bernhard Boehm; Domenico Bosco; Heinz Döbeli; Ina Stützer; Haiyan Wang; Markus Stoffel
Bace2 is a β cell-enriched protease that regulates pancreatic β cell function and mass.
Cell metabolism 2011;14(3):365-77.
2011: Gilbert S Omenn; Mark S Baker; Ruedi Aebersold
Recent Workshops of the HUPO Human Plasma Proteome Project (HPPP): a bridge with the HUPO CardioVascular Initiative and the emergence of SRM targeted proteomics.
Proteomics 2011;11(17):3439-43.
2011: Danilo Ritz; Sabina Schütz; Maja Vuk; Conrad C Weihl; Ruedi Aebersold; Robert H Baloh; Sebastian Bremer; Monika Bug; Timo Glatter; Matthias Gstaiger; Arnold Hayer; Philipp Kirchner; Houkeun Lee; Caleb Lusk; Hemmo Meyer
Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations.
Nature cell biology 2011;13(9):1116-23.
2011: Terry Farrah; Jonathan E Katz; Lin Biao; Parag Mallick; Johan Malmström; Robert L Moritz; Gilbert S Omenn; Reto Ossola; Zhi Sun; Julian D Watts; HUI ZHANG; Julie A Bletz; David S Campbell; Eric Deutsch; Ruedi Aebersold
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas.
Molecular & cellular proteomics : MCP 2011;10(9):M110.006353.
2011: Kaisa Kisko; Veli-Matti Leppänen; Andreas Menzel; John Missimer; Thomas Schleier; Thomas Walzthoeni; Ruedi Aebersold; Kari Alitalo; Maurice S Brozzo; Kurt Ballmer-Hofer
Structural analysis of vascular endothelial growth factor receptor-2/ligand complexes by small-angle X-ray solution scattering.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2011;25(9):2980-6.
2011: Rubén M Buey; Ilya Grigoriev; Kris Leslie; Erik Meijering; Andreas Menzel; John H Missimer; Renu Mohan; Ihor Smal; Ruedi Aebersold; Anna Akhmanova; Katja Bargsten; Sasa Bjelic; Thomas Walzthoeni; Michel O Steinmetz
Insights into EB1 structure and the role of its C-terminal domain for discriminating microtubule tips from the lattice.
Molecular biology of the cell 2011;22(16):2912-23.
2011: Lars Malmström; Johan Malmström; Ruedi Aebersold
Quantitative proteomics of microbes: Principles and applications to virulence.
Proteomics 2011;11(15):2947-56.
2011: Abdullah Kahraman; Lars Malmström; Ruedi Aebersold
Xwalk: computing and visualizing distances in cross-linking experiments.
Bioinformatics (Oxford, England) 2011;27(15):2163-4.
2011: Henry Lam; Ruedi Aebersold
Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics.
Methods (San Diego, Calif.) 2011;54(4):424-31.
2011: Pierre Legrain; György Marko-Varga; Ruedi Aebersold; Alexander Archakov; Amos Bairoch; Kumar Bala; Laura Beretta; John Bergeron; Christoph H Borchers; Garry L Corthals; Catherine E Costello; Eric W Deutsch; Bruno Domon; William Hancock; Fuchu He; Denis Hochstrasser; Young-Ki Paik; Ghasem Hosseini Salekdeh; Salvatore Sechi; Michael Snyder; Sudhir Srivastava; Mathias Uhlén; Cathy H Wu; Tadashi Yamamoto; Gilbert S Omenn
The human proteome project: current state and future direction.
Molecular & cellular proteomics : MCP 2011;10(7):M111.009993.
2011: Ariel Bensimon; Ruedi Aebersold; Yosef Shiloh
Beyond ATM: the protein kinase landscape of the DNA damage response.
FEBS letters 2011;585(11):1625-39.
2011: Lukas Reiter; Oliver Rinner; Paola Picotti; Ruth Hüttenhain; Martin Beck; Mi-Youn Brusniak; Michael O Hengartner; Ruedi Aebersold
mProphet: automated data processing and statistical validation for large-scale SRM experiments.
Nature methods 2011;8(5):430-5.
2011: Manfred Claassen; Ruedi Aebersold; Joachim M Buhmann
Proteome coverage prediction for integrated proteomics datasets.
Journal of computational biology : a journal of computational molecular cell biology 2011;18(3):283-93.
2011: Nathalie Selevsek; Mariette Matondo; Ruedi Aebersold; Marta Sanchez Carbayo; Bruno Domon
Systematic quantification of peptides/proteins in urine using selected reaction monitoring.
Proteomics 2011;11(6):1135-47.
2011: Wei Yan; Jie Luo; Max Robinson; Jimmy Eng; Ruedi Aebersold; Jeffrey Ranish
Index-ion triggered MS2 ion quantification: a novel proteomics approach for reproducible detection and quantification of targeted proteins in complex mixtures.
Molecular & cellular proteomics : MCP 2011;10(3):M110.005611.
2011: Igor Cima; Ralph Schiess; Peter Wild; Martin Kaelin; Peter Schüffler; Vinzenz Lange; Paola Picotti; Reto Ossola; Arnoud Templeton; Olga Schubert; Thomas Fuchs; Thomas Leippold; Stephen Wyler; Jens Zehetner; Wolfram Jochum; Joachim Buhmann; Thomas Cerny; Holger Moch; Silke Gillessen; Ruedi Aebersold; Wilhelm Krek
Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(8):3342-7.
2011: Eva Laurell; Katja Beck; Ksenia Krupina; Gandhi Theerthagiri; Bernd Bodenmiller; Peter Horvath; Ruedi Aebersold; Wolfram Antonin; Ulrike Kutay
Phosphorylation of Nup98 by multiple kinases is crucial for NPC disassembly during mitotic entry.
Cell 2011;144(4):539-50.
2011: Roeland Costenoble; Paola Picotti; Lukas Reiter; Robert Stallmach; Matthias Heinemann; Uwe Sauer; Ruedi Aebersold
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics.
Molecular systems biology 2011;7():464.
2011: Martin Beck; Manfred Claassen; Ruedi Aebersold
Comprehensive proteomics.
Current opinion in biotechnology 2011;22(1):3-8.
2011: Reiko Kiyonami; Alan Schoen; Amol Prakash; Scott Peterman; Vlad Zabrouskov; Paola Picotti; Ruedi Aebersold; Andreas Huhmer; Bruno Domon
Increased selectivity, analytical precision, and throughput in targeted proteomics.
Molecular & cellular proteomics : MCP 2011;10(2):M110.002931.
2011: Silvia Surinova; Ralph Schiess; Ruth Hüttenhain; Ferdinando Cerciello; Bernd Wollscheid; Ruedi Aebersold
On the development of plasma protein biomarkers.
Journal of proteome research 2011;10(1):5-16.
2011: Angela Bauch; Christian Beisel; Piotr Buczek; Franz-Josef Elmer; Kaloyan Enimanev; Pawel Glyzewski; Manuel Kohler; Lars Malmström; Tomasz Pylak; Andreas Quandt; Chandrasekhar Ramakrishnan; Izabela Adamczyk; Ruedi Aebersold; Bernd Rinn
openBIS: a flexible framework for managing and analyzing complex data in biology research.
BMC bioinformatics 2011;12():468.
2011: Martin Beck; Manfred Claassen; Jan Ellenberg; Franz Herzog; Johan Malmstroem; Alessandro Ori; Oliver Rinner; Alexander Schmidt; Anna Szymborska; Ruedi Aebersold
The quantitative proteome of a human cell line.
Molecular systems biology 2011;7():549.
2011: Timo Glatter; Ruedi Aebersold; Hyungwon Choi; Ernst Hafen; Irena Jevtov; Martin A Jünger; Katja Köhler; Alexey I Nesvizhskii; Oliver Rinner; Katarzyna Roguska; Ralf B Schittenhelm; Alexander Schmidt; Hugo Stocker; Alexander Wepf; Matthias Gstaiger
Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome.
Molecular systems biology 2011;7():547.
2011: Jie Zhang; Stefania Vaga; Goutham N Vemuri; Ruedi Aebersold; Pramote Chumnanpuen; Rahul Kumar; Jens Nielsen
Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae.
Molecular systems biology 2011;7():545.
2011: Tobias Maier; Alexander Schmidt; Ruedi Aebersold; Anne-Claude Gavin; Marc Güell; Sebastian Kühner; Luis Serrano
Quantification of mRNA and protein and integration with protein turnover in a bacterium.
Molecular systems biology 2011;7():511.
2011: Alexander Schmidt; Martin Beck; David Campbell; Manfred Claassen; Henry Lam; Johan Malmström; Ruedi Aebersold
Absolute quantification of microbial proteomes at different states by directed mass spectrometry.
Molecular systems biology 2011;7():510.
2011: Terry Farrah; Eric Deutsch; Ruedi Aebersold
Using the Human Plasma PeptideAtlas to study human plasma proteins.
Methods in molecular biology (Clifton, N.J.) 2011;728():349-74.
2011: Reto Ossola; Ralph Schiess; Paola Picotti; Oliver Rinner; Lukas Reiter; Ruedi Aebersold
Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites.
Methods in molecular biology (Clifton, N.J.) 2011;728():179-94.
2011: Mi-Youn K Brusniak; Sung-Tat Kwok; Mark Christiansen; David Campbell; Lukas Reiter; Paola Picotti; Ulrike Kusebauch; Hector Ramos; Eric Deutsch; Jingchun Chen; Robert L Moritz; Ruedi Aebersold
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.
BMC bioinformatics 2011;12():78.
2011: Tanja Scherrer; Ralph Schiess; Ruedi Aebersold; Christian Femmer; André P Gerber
Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins.
Genome biology 2011;12(1):R3.
2011: Hector Ramos; Paul Shannon; Mi-Youn Brusniak; Ulrike Kusebauch; Robert L Moritz; Ruedi Aebersold
The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage.
Proteomics 2011;11(1):154-8.
2011: Bernd Bodenmiller; Ruedi Aebersold
Phosphoproteome resource for systems biology research.
Methods in molecular biology (Clifton, N.J.) 2011;694():307-22.
2011: Sheng Pan; Ru Chen; Ruedi Aebersold; Teresa A Brentnall
Mass spectrometry based glycoproteomics--from a proteomics perspective.
Molecular & cellular proteomics : MCP 2011;10(1):R110.003251.
2010: Stefan Bohn; Florian Beck; Eri Sakata; Thomas Walzthoeni; Martin Beck; Ruedi Aebersold; Friedrich Förster; Wolfgang Baumeister; Stephan Nickell
Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(49):20992-7.
2010: Sourav Bandyopadhyay; Monika Mehta; Dwight Kuo; Min-Kyung Sung; Ryan Chuang; Eric J Jaehnig; Bernd Bodenmiller; Katherine Licon; Wilbert Copeland; Michael Shales; Dorothea Fiedler; Janusz Dutkowski; Aude Guénolé; Haico Van Attikum; Kevan M Shokat; Richard D Kolodner; Won-Ki Huh; Ruedi Aebersold; Michael-Christopher Keogh; Nevan J Krogan; Trey Ideker
Rewiring of genetic networks in response to DNA damage.
Science (New York, N.Y.) 2010;330(6009):1385-9.
2010: Christian H Ahrens; Erich Brunner; Ermir Qeli; Konrad Basler; Ruedi Aebersold
Generating and navigating proteome maps using mass spectrometry.
Nature reviews. Molecular cell biology 2010;11(11):789-801.
2010: Christian H Ahrens; Sabine P Schrimpf; Erich Brunner; Ruedi Aebersold
Model organism proteomics.
Journal of proteomics 2010;73(11):2051-3.
2010: Marko Jovanovic; Lukas Reiter; Paola Picotti; Vinzenz Lange; Erica Bogan; Benjamin A Hurschler; Cherie Blenkiron; Nicolas J Lehrbach; Xavier C Ding; Manuel Weiss; Sabine P Schrimpf; Eric A Miska; Helge Grosshans; Ruedi Aebersold; Michael O Hengartner
A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans.
Nature methods 2010;7(10):837-42.
2010: Cédric Przybylski; Martin A Jünger; Johannes Aubertin; François Radvanyi; Ruedi Aebersold; Delphine Pflieger
Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-Orbitrap instrument.
Journal of proteome research 2010;9(10):5118-32.
2010: Hamid Mirzaei; Richard S Rogers; Barbara Grimes; Jimmy Eng; Alan Aderem; Ruedi Aebersold
Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry.
Molecular bioSystems 2010;6(10):2004-14.
2010: Tommy Nilsson; Matthias Mann; Ruedi Aebersold; John R Yates; Amos Bairoch; John J M Bergeron
Mass spectrometry in high-throughput proteomics: ready for the big time.
Nature methods 2010;7(9):681-5.
2010: Alexander Leitner; Thomas Walzthoeni; Abdullah Kahraman; Franz Herzog; Oliver Rinner; Martin Beck; Ruedi Aebersold
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics.
Molecular & cellular proteomics : MCP 2010;9(8):1634-49.
2010: Bruno Domon; Ruedi Aebersold
Options and considerations when selecting a quantitative proteomics strategy.
Nature biotechnology 2010;28(7):710-21.
2010: Mark W Duncan; Ruedi Aebersold; Richard M Caprioli
The pros and cons of peptide-centric proteomics.
Nature biotechnology 2010;28(7):659-64.
2010: Anne Kümmel; Jennifer Christina Ewald; Sarah-Maria Fendt; Stefan Jasper Jol; Paola Picotti; Ruedi Aebersold; Uwe Sauer; Nicola Zamboni; Matthias Heinemann
Differential glucose repression in common yeast strains in response to HXK2 deletion.
FEMS yeast research 2010;10(3):322-32.
2010: Henry Lam; Ruedi Aebersold
Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2010;Chapter 25():Unit 25.5.
2010: Eric Deutsch; Luis Mendoza; David Shteynberg; Terry Farrah; Henry Lam; Natalie Tasman; Zhi Sun; Erik Nilsson; Brian Pratt; Bryan Prazen; Jimmy K Eng; Daniel B Martin; Alexey I Nesvizhskii; Ruedi Aebersold
A guided tour of the Trans-Proteomic Pipeline.
Proteomics 2010;10(6):1150-9.
2010: Eric Deutsch; David Shteynberg; Henry Lam; Zhi Sun; Jimmy K Eng; Christine Carapito; Priska D von Haller; Natalie Tasman; Luis Mendoza; Terry Farrah; Ruedi Aebersold
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.
Proteomics 2010;10(6):1190-5.
2010: David K Breslow; Sean R Collins; Bernd Bodenmiller; Ruedi Aebersold; Kai Simons; Andrej Shevchenko; Christer S Ejsing; Jonathan S Weissman
Orm family proteins mediate sphingolipid homeostasis.
Nature 2010;463(7284):1048-53.
2010: Margret H Bülow; Ruedi Aebersold; Michael J Pankratz; Martin A Jünger
The Drosophila FoxA ortholog Fork head regulates growth and gene expression downstream of Target of rapamycin.
PloS one 2010;5(12):e15171.
2010: Bernd Bodenmiller; Stefanie Wanka; Claudine Kraft; Jörg Urban; David Campbell; Patrick G Pedrioli; Bertran Gerrits; Paola Picotti; Henry Lam; Olga Vitek; Mi-Youn Brusniak; Bernd Roschitzki; Chao Zhang; Kevan M Shokat; Ralph Schlapbach; Alejandro Colman-Lerner; Garry P Nolan; Alexey I Nesvizhskii; Matthias Peter; Robbie Loewith; Christian von Mering; Ruedi Aebersold
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.
Science signaling 2010;3(153):rs4.
2010: Ariel Bensimon; Alexander Schmidt; Yael Ziv; Ran Elkon; Shih-Ya Wang; David J Chen; Ruedi Aebersold; Yosef Shiloh
ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage.
Science signaling 2010;3(151):rs3.
2010: Bernd Bodenmiller; Ruedi Aebersold
Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics.
Methods in enzymology 2010;470():317-34.
2010: Henry Lam; Ruedi Aebersold
Spectral library searching for peptide identification via tandem MS.
Methods in molecular biology (Clifton, N.J.) 2010;604():95-103.
2010: Paola Picotti; Oliver Rinner; Robert Stallmach; Franziska Dautel; Terry Farrah; Bruno Domon; Holger Wenschuh; Ruedi Aebersold
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes.
Nature methods 2010;7(1):43-6.
2010: Henry Lam; Eric W Deutsch; Ruedi Aebersold
Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics.
Journal of proteome research 2010;9(1):605-10.
2009: Ruth Hüttenhain; Johan Malmström; Paola Picotti; Ruedi Aebersold
Perspectives of targeted mass spectrometry for protein biomarker verification.
Current opinion in chemical biology 2009;13(5-6):518-25.
2009: Alexander Schmidt; Manfred Claassen; Ruedi Aebersold
Directed mass spectrometry: towards hypothesis-driven proteomics.
Current opinion in chemical biology 2009;13(5-6):510-7.
2009: Sebastian Kühner; Vera van Noort; Matthew J Betts; Alejandra Leo-Macias; Claire Batisse; Michaela Rode; Takuji Yamada; Tobias Maier; Samuel Bader; Pedro Beltran-Alvarez; Daniel Castaño-Diez; Wei-Hua Chen; Damien Devos; Marc Güell; Tomas Norambuena; Ines Racke; Vladimir Rybin; Alexander Schmidt; Eva Yus; Ruedi Aebersold; Richard Herrmann; Bettina Böttcher; Achilleas S Frangakis; Robert B Russell; Luis Serrano; Peer Bork; Anne-Claude Gavin
Proteome organization in a genome-reduced bacterium.
Science (New York, N.Y.) 2009;326(5957):1235-40.
2009: Sandra Goetze; Ermir Qeli; Christian Mosimann; An Staes; Bertran Gerrits; Bernd Roschitzki; Sonali Mohanty; Eva M Niederer; Endre Laczko; Evy Timmerman; Vinzenz Lange; Ernst Hafen; Ruedi Aebersold; Joël Vandekerckhove; Konrad Basler; Christian H Ahrens; Kris Gevaert; Erich Brunner
Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster.
PLoS biology 2009;7(11):e1000236.
2009: Martin Beck; Johan A Malmström; Vinzenz Lange; Alexander Schmidt; Eric W Deutsch; Ruedi Aebersold
Visual proteomics of the human pathogen Leptospira interrogans.
Nature methods 2009;6(11):817-23.
2009: Lukas Reiter; Manfred Claassen; Sabine P Schrimpf; Marko Jovanovic; Alexander Schmidt; Joachim M Buhmann; Michael O Hengartner; Ruedi Aebersold
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry.
Molecular & cellular proteomics : MCP 2009;8(11):2405-17.
2009: Carly A Sherwood; Ashley Eastham; Lik Wee Lee; Amelia Peterson; Jimmy K Eng; David Shteynberg; Luis Mendoza; Eric W Deutsch; Jenni Risler; Natalie Tasman; Ruedi Aebersold; Henry Lam; Daniel B Martin
MaRiMba: a software application for spectral library-based MRM transition list assembly.
Journal of proteome research 2009;8(10):4396-405.
2009: Matthias Gstaiger; Ruedi Aebersold
Applying mass spectrometry-based proteomics to genetics, genomics and network biology.
Nature reviews. Genetics 2009;10(9):617-27.
2009: Paola Picotti; Bernd Bodenmiller; Lukas N Mueller; Bruno Domon; Ruedi Aebersold
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics.
Cell 2009;138(4):795-806.
2009: Alexandre Huber; Bernd Bodenmiller; Aino Uotila; Michael Stahl; Stefanie Wanka; Bertran Gerrits; Ruedi Aebersold; Robbie Loewith
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.
Genes & development 2009;23(16):1929-43.
2009: Johan Malmström; Martin Beck; Alexander Schmidt; Vinzenz Lange; Eric W Deutsch; Ruedi Aebersold
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans.
Nature 2009;460(7256):762-5.
2009: Martin Eisenacher; Lennart Martens; Tanja Hardt; Michael Kohl; Harald Barsnes; Kenny Helsens; Jari Häkkinen; Fredrik Levander; Ruedi Aebersold; Joël Vandekerckhove; Michael J Dunn; Frederique Lisacek; Jennifer A Siepen; Simon J Hubbard; Pierre-Alain Binz; Martin Blüggel; Herbert Thiele; John Cottrell; Helmut E Meyer; Rolf Apweiler; Christian Stephan
Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Proteomics 2009;9(15):3928-33.
2009: Hamid Mirzaei; Mi-Youn Brusniak; Lukas N Mueller; Simon Letarte; Julian D Watts; Ruedi Aebersold
Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry.
Molecular & cellular proteomics : MCP 2009;8(8):1934-46.
2009: Seul-Ki Jeong; Min-Seok Kwon; Eun-Young Lee; Hyoung-Joo Lee; Sang Yun Cho; Hoguen Kim; Jong Shin Yoo; Gilbert S Omenn; Ruedi Aebersold; Sam Hanash; Young-Ki Paik
BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers.
Proteomics 2009;9(14):3729-40.
2009: Manfred Claassen; Ruedi Aebersold; Joachim M Buhmann
Proteome coverage prediction with infinite Markov models.
Bioinformatics (Oxford, England) 2009;25(12):i154-60.
2009: Ruedi Aebersold
A stress test for mass spectrometry-based proteomics.
Nature methods 2009;6(6):411-2.
2009: Bruno Domon; Bernd Bodenmiller; Christine Carapito; Zhiqi Hao; Andreas Huehmer; Ruedi Aebersold
Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome.
Journal of proteome research 2009;8(6):2633-9.
2009: Christine Carapito; Clementine Klemm; Ruedi Aebersold; Bruno Domon
Systematic LC-MS analysis of labile post-translational modifications in complex mixtures.
Journal of proteome research 2009;8(5):2608-14.
2009: N Leigh Anderson; Norman G Anderson; Terry W Pearson; Christoph H Borchers; Amanda G Paulovich; Scott D Patterson; Michael Gillette; Ruedi Aebersold; Steven A Carr
A human proteome detection and quantitation project.
Molecular & cellular proteomics : MCP 2009;8(5):883-6.
2009: Sheng Pan; Ru Chen; Beth Ann Reimel; David A Crispin; Hamid Mirzaei; Kelly Cooke; Joshua F Coleman; Zhaoli Lane; Mary P Bronner; David R Goodlett; Martin W McIntosh; William Traverso; Ruedi Aebersold; Teresa A Brentnall
Quantitative proteomics investigation of pancreatic intraepithelial neoplasia.
Electrophoresis 2009;30(7):1132-44.
2009: Bernd Wollscheid; Damaris Bausch-Fluck; Christine Henderson; Robert O'Brien; Miriam Bibel; Ralph Schiess; Ruedi Aebersold; Julian D Watts
Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins.
Nature biotechnology 2009;27(4):378-86.
2009: Ralph Schiess; Lukas N Mueller; Alexander Schmidt; Markus Mueller; Bernd Wollscheid; Ruedi Aebersold
Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry.
Molecular & cellular proteomics : MCP 2009;8(4):624-38.
2009: Sebastian Leidel; Patrick G A Pedrioli; Tamara Bucher; Renée Brost; Michael Costanzo; Alexander Schmidt; Ruedi Aebersold; Charles Boone; Kay Hofmann; Matthias Peter
Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA.
Nature 2009;458(7235):228-32.
2009: Sabine P Schrimpf; Manuel Weiss; Lukas Reiter; Christian H Ahrens; Marko Jovanovic; Johan Malmström; Erich Brunner; Sonali Mohanty; Martin J Lercher; Peter Hunziker; Ruedi Aebersold; Christian von Mering; Michael O. Hengartner
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.
PLoS biology 2009;7(3):e48.
2009: Alexander Wepf; Timo Glatter; Alexander Schmidt; Ruedi Aebersold; Matthias Gstaiger
Quantitative interaction proteomics using mass spectrometry.
Nature methods 2009;6(3):203-5.
2009: Nils Gehlenborg; Wei Yan; Inyoul Y Lee; Hyuntae Yoo; Kay Nieselt; Daehee Hwang; Ruedi Aebersold; Leroy Hood
Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.
Bioinformatics (Oxford, England) 2009;25(5):682-3.
2009: Wei Yan; Ruedi Aebersold; Elaine W Raines
Evolution of organelle-associated protein profiling.
Journal of proteomics 2009;72(1):4-11.
2009: Ralph Schiess; Bernd Wollscheid; Ruedi Aebersold
Targeted proteomic strategy for clinical biomarker discovery.
Molecular oncology 2009;3(1):33-44.
2009: Sheng Pan; Ruedi Aebersold; Ru Chen; John Rush; David R Goodlett; Martin W McIntosh; Jing Zhang; Teresa A Brentnall
Mass spectrometry based targeted protein quantification: methods and applications.
Journal of proteome research 2009;8(2):787-97.
2009: Peter Ulintz; Anastasia K Yocum; Bernd Bodenmiller; Ruedi Aebersold; Philip C Andrews; Alexey I Nesvizhskii
Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification.
Journal of proteome research 2009;8(2):887-99.
2009: Chris Soon Heng Tan; Bernd Bodenmiller; Adrian Pasculescu; Marko Jovanovic; Michael O Hengartner; Claus Jørgensen; Gary D Bader; Ruedi Aebersold; Tony Pawson; Rune Linding
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases.
Science signaling 2009;2(81):ra39.
2009: Sandra N Loevenich; Erich Brunner; Nichole L King; Eric W Deutsch; Stephen E Stein; Ruedi Aebersold; Ernst Hafen
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
BMC bioinformatics 2009;10():59.
2009: Timo Glatter; Alexander Wepf; Ruedi Aebersold; Matthias Gstaiger
An integrated workflow for charting the human interaction proteome: insights into the PP2A system.
Molecular systems biology 2009;5():237.
2009: Gilbert S Omenn; Ruedi Aebersold; Young-Ki Paik
7(th) HUPO World Congress of Proteomics: launching the second phase of the HUPOPlasma Proteome Project (PPP-2) 16-20 August 2008, Amsterdam, The Netherlands.
Proteomics 2009;9(1):4-6.
2009: Simon Urwyler; Yves Nyfeler; Curdin Ragaz; Hookeun Lee; Lukas N Mueller; Ruedi Aebersold; Hubert Hilbi
Proteome analysis of Legionella vacuoles purified by magnetic immunoseparation reveals secretory and endosomal GTPases.
Traffic (Copenhagen, Denmark) 2009;10(1):76-87.
2009: Marilyn Goudreault; Lisa M D'Ambrosio; Michelle J Kean; Michael J Mullin; Brett G Larsen; Amy Sanchez; Sidharth Chaudhry; Ginny I Chen; Frank Sicheri; Alexey I Nesvizhskii; Ruedi Aebersold; Brian Raught; Anne-Claude Gingras
A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein.
Molecular & cellular proteomics : MCP 2009;8(1):157-71.
2008: Bernd Bodenmiller; David Campbell; Bertran Gerrits; Henry Lam; Marko Jovanovic; Paola Picotti; Ralph Schlapbach; Ruedi Aebersold
PhosphoPep--a database of protein phosphorylation sites in model organisms.
Nature biotechnology 2008;26(12):1339-40.
2008: Daehee Hwang; Ning Zhang; Hookeun Lee; Eugene Yi; HUI ZHANG; Inyoul Y Lee; Leroy Hood; Ruedi Aebersold
MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis.
Bioinformatics (Oxford, England) 2008;24(22):2641-2.
2008: Anne-Claude Gavin; Ruedi Aebersold; Albert J R Heck
Meeting report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology.
Molecular & cellular proteomics : MCP 2008;7(11):2288-91.
2008: Paola Picotti; Henry Lam; David Campbell; Eric W Deutsch; Hamid Mirzaei; Jeff Ranish; Bruno Domon; Ruedi Aebersold
A database of mass spectrometric assays for the yeast proteome.
Nature methods 2008;5(11):913-4.
2008: Alexander Schmidt; Nils Gehlenborg; Bernd Bodenmiller; Lukas N Mueller; Dave Campbell; Markus Mueller; Ruedi Aebersold; Bruno Domon
An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures.
Molecular & cellular proteomics : MCP 2008;7(11):2138-50.
2008: Henry Lam; Eric W Deutsch; James S Eddes; Jimmy K Eng; Stephen E Stein; Ruedi Aebersold
Building consensus spectral libraries for peptide identification in proteomics.
Nature methods 2008;5(10):873-5.
2008: Christopher Taylor; Pierre-Alain Binz; Ruedi Aebersold; Michel Affolter; Robert Barkovich; Eric W Deutsch; David M Horn; Andreas Hühmer; Martin Kussmann; Kathryn Lilley; Marcus Macht; Matthias Mann; Dieter Müller; Thomas A Neubert; Janice Nickson; Scott D Patterson; Roberto Raso; Kathryn Resing; Sean L Seymour; Akira Tsugita; Ioannis Xenarios; Rong Zeng; Randall K Julian
Guidelines for reporting the use of mass spectrometry in proteomics.
Nature biotechnology 2008;26(8):860-1.
2008: 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
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring.
Molecular & cellular proteomics : MCP 2008;7(8):1489-500.
2008: Eric D Rubio; David J Reiss; Piri Welcsh; Christine M Disteche; Galina N Filippova; Nitin S Baliga; Ruedi Aebersold; Jeffrey A Ranish; Anton Krumm
CTCF physically links cohesin to chromatin.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(24):8309-14.
2008: Eric W Deutsch; Henry Lam; Ruedi Aebersold
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.
EMBO reports 2008;9(5):429-34.
2008: Alex Soltermann; Reto Ossola; Sandra Kilgus-Hawelski; Arnold von Eckardstein; Tobias Suter; Ruedi Aebersold; Holger Moch
N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics.
Cancer 2008;114(2):124-33.
2008: Oliver Rinner; Jan Seebacher; Thomas Walzthoeni; Lukas N Mueller; Martin Beck; Alexander Schmidt; Markus Mueller; Ruedi Aebersold
Identification of cross-linked peptides from large sequence databases.
Nature methods 2008;5(4):315-8.
2008: Hamid Mirzaei; Joshua K McBee; Julian Watts; Ruedi Aebersold
Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics.
Molecular & cellular proteomics : MCP 2008;7(4):813-23.
2008: Eric Deutsch; Henry Lam; Ruedi Aebersold
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.
Physiological genomics 2008;33(1):18-25.
2008: Yingchuan Qi; Jeffrey A Ranish; Xiaoyan Zhu; Anna Krones; Jie Zhang; Ruedi Aebersold; David W Rose; Michael G Rosenfeld; C Carrière
Atbf1 is required for the Pit1 gene early activation.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(7):2481-6.
2008: Zhiqing Zou; Marta Ibisate; Yong Zhou; Ruedi Aebersold; Younan Xia; Hui Zhang
Synthesis and evaluation of superparamagnetic silica particles for extraction of glycopeptides in the microtiter plate format.
Analytical chemistry 2008;80(4):1228-34.
2008: Delphine Pflieger; Martin A Jünger; Markus Müller; Oliver Rinner; Hookeun Lee; Peter M Gehrig; Matthias Gstaiger; Ruedi Aebersold
Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation.
Molecular & cellular proteomics : MCP 2008;7(2):326-46.
2008: Mi-Youn Brusniak; Bernd Bodenmiller; David Campbell; Kelly Cooke; James Eddes; Andrew Garbutt; Hollis Lau; Simon Letarte; Lukas N Mueller; Vagisha Sharma; Olga Vitek; Ning Zhang; Ruedi Aebersold; Julian D Watts
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.
BMC bioinformatics 2008;9():542.
2008: Michael L Tress; Bernd Bodenmiller; Ruedi Aebersold; Carmen Galvez
Proteomics studies confirm the presence of alternative protein isoforms on a large scale.
Genome biology 2008;9(11):R162.
2008: Vinzenz Lange; Paola Picotti; Bruno Domon; Ruedi Aebersold
Selected reaction monitoring for quantitative proteomics: a tutorial.
Molecular systems biology 2008;4():222.
2008: Yong Chi; Markus Welcker; Asli A Hizli; Jeffrey J Posakony; Ruedi Aebersold; Bruce E Clurman
Identification of CDK2 substrates in human cell lysates.
Genome biology 2008;9(10):R149.
2008: Qing Zhang; Rajasree Menon; Eric W Deutsch; Sharon J Pitteri; Vitor M Faca; Hong Wang; Lisa F Newcomb; Ronald A DePinho; Nabeel Bardeesy; Daniela M Dinulescu; Kenneth E Hung; Raju Kucherlapati; Tyler Jacks; Katerina Politi; Ruedi Aebersold; Gilbert S Omenn; David States; Samir M Hanash
A mouse plasma peptide atlas as a resource for disease proteomics.
Genome biology 2008;9(6):R93.
2008: Wei Yan; Daehee Hwang; Ruedi Aebersold
Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins.
Methods in molecular biology (Clifton, N.J.) 2008;432():389-401.
2008: Lukas Mueller; Mi-Youn Brusniak; D R Mani; Ruedi Aebersold
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.
Journal of proteome research 2008;7(1):51-61.
2008: Peter Ulintz; Bernd Bodenmiller; Philip C Andrews; Ruedi Aebersold; Alexey I Nesvizhskii
Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence.
Molecular & cellular proteomics : MCP 2008;7(1):71-87.
2008: John Klimek; James S Eddes; Laura Hohmann; Jennifer Jackson; Amelia Peterson; Simon Letarte; Philip R Gafken; Jonathan E Katz; Parag Mallick; Hookeun Lee; Alexander Schmidt; Reto Ossola; Jimmy K Eng; Ruedi Aebersold; Daniel B Martin
The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.
Journal of proteome research 2008;7(1):96-103.
2007: Nabil Djouder; Stefan Christian Metzler; Alexander Schmidt; Christiane Wirbelauer; Matthias Gstaiger; Ruedi Aebersold; daniel Hess; Wilhelm Krek
S6K1-mediated disassembly of mitochondrial URI/PP1gamma complexes activates a negative feedback program that counters S6K1 survival signaling.
Molecular cell 2007;28(1):28-40.
2007: Bong Kim; Alexey I Nesvizhskii; P Geetha Rani; Steven Hahn; Ruedi Aebersold; Jeffrey A Ranish
The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(41):16068-73.
2007: Andrew R Jones; Michael Miller; Ruedi Aebersold; Rolf Apweiler; Catherine A Ball; Alvis Brazma; James Degreef; Nigel Hardy; Henning Hermjakob; Simon Hubbard; Peter Hussey; Mark Igra; Helen Jenkins; Randall K Julian; Kent Laursen; Stephen G Oliver; Norman W Paton; Susanna-Assunta Sansone; Ugis Sarkans; Christian J Stoeckert; Christopher Taylor; Patricia L Whetzel; Joseph A White; Paul Spellman; Angel Pizarro
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Nature biotechnology 2007;25(10):1127-33.
2007: Alexey I Nesvizhskii; Olga Vitek; Ruedi Aebersold
Analysis and validation of proteomic data generated by tandem mass spectrometry.
Nature methods 2007;4(10):787-97.
2007: Lukas Mueller; Oliver Rinner; Alexander Schmidt; Simon Letarte; Bernd Bodenmiller; Mi-Youn Brusniak; Olga Vitek; Ruedi Aebersold; Markus Müller
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling.
Proteomics 2007;7(19):3470-80.
2007: Hans Noll; Joy Alcedo; Michael Daube; Erich Frei; Emile Schiltz; John Hunt; Tom Humphries; Valeria Matranga; Martin Hochstrasser; Ruedi Aebersold; Hookeun Lee; Markus Noll
The toposome, essential for sea urchin cell adhesion and development, is a modified iron-less calcium-binding transferrin.
Developmental biology 2007;310(1):54-70.
2007: Jianru Stahl-Zeng; Vinzenz Lange; Reto Ossola; Katrin Eckhardt; Wilhelm Krek; Ruedi Aebersold; Bruno Domon
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites.
Molecular & cellular proteomics : MCP 2007;6(10):1809-17.
2007: Amol Prakash; Brian Piening; Jeffrey Whiteaker; Heidi Zhang; Scott A Shaffer; Daniel Martin; Laura Hohmann; Kelly Cooke; James M Olson; Stacey Hansen; Mark R Flory; Hookeun Lee; Julian Watts; David R Goodlett; Ruedi Aebersold; Amanda Paulovich; Benno Schwikowski
Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics.
Molecular & cellular proteomics : MCP 2007;6(10):1741-8.
2007: Paola Picotti; Ruedi Aebersold; Bruno Domon
The implications of proteolytic background for shotgun proteomics.
Molecular & cellular proteomics : MCP 2007;6(9):1589-98.
2007: Celina Demers; Chandra-Prakash Chaturvedi; Jeffrey A Ranish; Gaetan Juban; Patrick Lai; Francois Morle; Ruedi Aebersold; F Jeffrey Dilworth; Mark Groudine; Marjorie Brand
Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus.
Molecular cell 2007;27(4):573-84.
2007: Johan Malmström; Hookeun Lee; Ruedi Aebersold
Advances in proteomic workflows for systems biology.
Current opinion in biotechnology 2007;18(4):378-84.
2007: Christopher Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric Deutsch; Michael J Dunn; albert heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
The minimum information about a proteomics experiment (MIAPE).
Nature biotechnology 2007;25(8):887-93.
2007: Anne-Claude Gingras; Matthias Gstaiger; Brian Raught; Ruedi Aebersold
Analysis of protein complexes using mass spectrometry.
Nature reviews. Molecular cell biology 2007;8(8):645-54.
2007: Yong Zhou; Ruedi Aebersold; HUI ZHANG
Isolation of N-linked glycopeptides from plasma.
Analytical chemistry 2007;79(15):5826-37.
2007: Ru Chen; Teresa A Brentnall; Sheng Pan; Kelly Cooke; Kara White Moyes; Zhaoli Lane; David A Crispin; David R Goodlett; Ruedi Aebersold; Mary P Bronner
Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer.
Molecular & cellular proteomics : MCP 2007;6(8):1331-42.
2007: Julie Lessard; Jiang I Wu; Jeffrey A Ranish; Mimi Wan; Monte M Winslow; Brett T Staahl; Hai Wu; Ruedi Aebersold; ISabella Graef; Gerald R Crabtree
An essential switch in subunit composition of a chromatin remodeling complex during neural development.
Neuron 2007;55(2):201-15.
2007: Edmund Au; Miranda W Richter; Adele J Vincent; Wolfram Tetzlaff; Ruedi Aebersold; E Helene Sage; A Jane Roskams
SPARC from olfactory ensheathing cells stimulates Schwann cells to promote neurite outgrowth and enhances spinal cord repair.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2007;27(27):7208-21.
2007: Christian H Ahrens; Erich Brunner; Ernst Hafen; Ruedi Aebersold; Konrad Basler
A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics.
Fly 2007;1(3):182-6.
2007: Erich Brunner; Christian H Ahrens; Sonali Mohanty; Hansruedi Baetschmann; Sandra Loevenich; Frank Potthast; Eric Deutsch; Christian Panse; Ulrik de Lichtenberg; Oliver Rinner; Hookeun Lee; Patrick G A Pedrioli; Johan Malmstrom; Katja Koehler; Sabine Schrimpf; Jeroen Krijgsveld; Floyd Kregenow; albert heck; Ernst Hafen; Ralph Schlapbach; Ruedi Aebersold
A high-quality catalog of the Drosophila melanogaster proteome.
Nature biotechnology 2007;25(5):576-83.
2007: Bernd Bodenmiller; Lukas Mueller; Patrick G A Pedrioli; Delphine Pflieger; Martin A Jünger; Jimmy K Eng; Ruedi Aebersold; W Andy Tao
An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells.
Molecular bioSystems 2007;3(4):275-86.
2007: Pei Wang; Hua Tang; Matthew Fitzgibbon; Martin McIntosh; Marc Coram; HUI ZHANG; Eugene Yi; Ruedi Aebersold
A statistical method for chromatographic alignment of LC-MS data.
Biostatistics (Oxford, England) 2007;8(2):357-67.
2007: Oliver Rinner; Lukas Mueller; Martin Hubálek; Markus Müller; Matthias Gstaiger; Ruedi Aebersold
An integrated mass spectrometric and computational framework for the analysis of protein interaction networks.
Nature biotechnology 2007;25(3):345-52.
2007: Henry Lam; Eric Deutsch; James S Eddes; Jimmy K Eng; Nichole King; Stephen E Stein; Ruedi Aebersold
Development and validation of a spectral library searching method for peptide identification from MS/MS.
Proteomics 2007;7(5):655-67.
2007: Bernd Bodenmiller; Lukas Mueller; Markus Mueller; Bruno Domon; Ruedi Aebersold
Reproducible isolation of distinct, overlapping segments of the phosphoproteome.
Nature methods 2007;4(3):231-7.
2007: Rohini Jasavala; Harryl Martinez; Jaykumar Thumar; Armann Andaya; Anne-Claude Gingras; Jimmy K Eng; Ruedi Aebersold; David K Han; Michael E Wright
Identification of putative androgen receptor interaction protein modules: cytoskeleton and endosomes modulate androgen receptor signaling in prostate cancer cells.
Molecular & cellular proteomics : MCP 2007;6(2):252-71.
2007: Ruedi Aebersold; Timothy J Griffin; Sam Donohoe
Isotope-coded affinity tagging of proteins.
CSH protocols 2007;2007():pdb.prot4728.
2007: Bernd Bodenmiller; Johan Malmstrom; Bertran Gerrits; David Campbell; Henry Lam; Alexander Schmidt; Oliver Rinner; Lukas Mueller; Paul T Shannon; Patrick G A Pedrioli; Christian Panse; Hoo-Keun Lee; Ralph Schlapbach; Ruedi Aebersold
PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.
Molecular systems biology 2007;3():139.
2007: Yu Lu; Patricia Bottari; Ruedi Aebersold; Frantisek Turecek; Michael H Gelb
Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags.
Methods in molecular biology (Clifton, N.J.) 2007;359():159-76.
2007: Jeffrey A Ranish; Marjorie Brand; Ruedi Aebersold
Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition.
Methods in molecular biology (Clifton, N.J.) 2007;359():17-35.
2007: Yuan Tian; Yong Zhou; Sarah Elliott; Ruedi Aebersold; HUI ZHANG
Solid-phase extraction of N-linked glycopeptides.
Nature protocols 2007;2(2):334-9.
2007: Ru Chen; Sheng Pan; Kelly Cooke; Kara White Moyes; Mary P Bronner; David R Goodlett; Ruedi Aebersold; Teresa A Brentnall
Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis.
Pancreas 2007;34(1):70-9.
2007: Parag Mallick; Markus Schirle; Sharon Chen; Mark R Flory; Hookeun Lee; Daniel Martin; Jeffrey A Ranish; Brian Raught; Robert Schmitt; Thilo Werner; Bernhard Kuster; Ruedi Aebersold
Computational prediction of proteotypic peptides for quantitative proteomics.
Nature biotechnology 2007;25(1):125-31.
2007: Sheng Pan; Ruedi Aebersold
Quantitative proteomics by stable isotope labeling and mass spectrometry.
Methods in molecular biology (Clifton, N.J.) 2007;367():209-18.
2007: HUI ZHANG; Alvin Y Liu; Paul Loriaux; Bernd Wollscheid; Yong Zhou; Julian D Watts; Ruedi Aebersold
Mass spectrometric detection of tissue proteins in plasma.
Molecular & cellular proteomics : MCP 2007;6(1):64-71.
2006: Mark R Flory; Hookeun Lee; Richard Bonneau; Parag Mallick; Kyle Serikawa; David R Morris; Ruedi Aebersold
Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents.
Proteomics 2006;6(23):6146-57.
2006: Bruno Domon; Ruedi Aebersold
Challenges and opportunities in proteomics data analysis.
Molecular & cellular proteomics : MCP 2006;5(10):1921-6.
2006: Jan Seebacher; Parag Mallick; Ning Zhang; James S Eddes; Ruedi Aebersold; Michael H Gelb
Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing.
Journal of proteome research 2006;5(9):2270-82.
2006: Johan Malmström; Hookeun Lee; Alexey I Nesvizhskii; David Shteynberg; Sonali Mohanty; Erich Brunner; Mingliang Ye; Gerhard Weber; Christoph Eckerskorn; Ruedi Aebersold
Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.
Journal of proteome research 2006;5(9):2241-9.
2006: Natalie T Rundle; Jim Nelson; Mark R Flory; Jomon Joseph; John Th'ng; Ruedi Aebersold; Mary Dasso; Raymond J Andersen; Michel Roberge
An ent-kaurene that inhibits mitotic chromosome movement and binds the kinetochore protein ran-binding protein 2.
ACS chemical biology 2006;1(7):443-50.
2006: Patrick G A Pedrioli; Brian Raught; Xiang-Dong Zhang; Richard Rogers; John Aitchison; Michael J Matunis; Ruedi Aebersold
Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software.
Nature methods 2006;3(7):533-9.
2006: Ru Chen; Sheng Pan; Eugene C Yi; Samuel Donohoe; Mary P Bronner; John D Potter; David R Goodlett; Ruedi Aebersold; Teresa A Brentnall
Quantitative proteomic profiling of pancreatic cancer juice.
Proteomics 2006;6(13):3871-9.
2006: Neetu Gupta; Bernd Wollscheid; Julian D Watts; Barbara Scheer; Ruedi Aebersold; Anthony L DeFranco
Quantitative proteomic analysis of B cell lipid rafts reveals that ezrin regulates antigen receptor-mediated lipid raft dynamics.
Nature immunology 2006;7(6):625-33.
2006: Rueichi R Gan; Eugene C Yi; Yulun Chiu; Hookeun Lee; Yu-Chieh P Kao; Timothy H Wu; Ruedi Aebersold; David R Goodlett; Wailap Victor Ng
Proteome analysis of Halobacterium sp. NRC-1 facilitated by the biomodule analysis tool BMSorter.
Molecular & cellular proteomics : MCP 2006;5(6):987-97.
2006: Ralph A Bradshaw; Al L Burlingame; Steven Carr; Ruedi Aebersold
Reporting protein identification data: the next generation of guidelines.
Molecular & cellular proteomics : MCP 2006;5(5):787-8.
2006: Marco Maccarana; Benny Pacheco; Johan Malmström; Kerstin Tiedemann; Ruedi Aebersold; Ulf Lindahl; Jin-Ping Li; Anders Malmström
Biosynthesis of dermatan sulfate: chondroitin-glucuronate C5-epimerase is identical to SART2.
The Journal of biological chemistry 2006;281(17):11560-8.
2006: Bruno Domon; Ruedi Aebersold
Mass spectrometry and protein analysis.
Science (New York, N.Y.) 2006;312(5771):212-7.
2006: Philip R Hardwidge; Samuel Donohoe; Ruedi Aebersold; B Brett Finlay
Proteomic analysis of the binding partners to enteropathogenic Escherichia coli virulence proteins expressed in Saccharomyces cerevisiae.
Proteomics 2006;6(7):2174-9.
2006: Alexey I Nesvizhskii; Franz F Roos; Jonas Grossmann; Mathijs Vogelzang; James S Eddes; Wilhelm Gruissem; Sacha Baginsky; Ruedi Aebersold
Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides.
Molecular & cellular proteomics : MCP 2006;5(4):652-70.
2006: Amol Prakash; Parag Mallick; Jeffrey Whiteaker; Heidi Zhang; Amanda Paulovich; Mark R Flory; Hookeun Lee; Ruedi Aebersold; Benno Schwikowski
Signal maps for mass spectrometry-based comparative proteomics.
Molecular & cellular proteomics : MCP 2006;5(3):423-32.
2006: Yuzuru Shiio; Kwang S Suh; Hookeun Lee; Stuart H Yuspa; Robert N Eisenman; Ruedi Aebersold
Quantitative proteomic analysis of myc-induced apoptosis: a direct role for Myc induction of the mitochondrial chloride ion channel, mtCLIC/CLIC4.
The Journal of biological chemistry 2006;281(5):2750-6.
2006: Yuzuru Shiio; David W Rose; Radin Aur; Samuel Donohoe; Ruedi Aebersold; Robert N Eisenman
Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex.
Molecular and cellular biology 2006;26(4):1386-97.
2006: Sandra Orchard; Henning Hermjakob; Chris Taylor; Pierre-Alain Binz; Christine Hoogland; Randall K Julian; John S Garavelli; Ruedi Aebersold; Rolf Apweiler
Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
Proteomics 2006;6(3):738-41.
2006: Yuzuru Shiio; Ruedi Aebersold
Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry.
Nature protocols 2006;1(1):139-45.
2006: Alexander Schmidt; Ruedi Aebersold
High-accuracy proteome maps of human body fluids.
Genome biology 2006;7(11):242.
2006: Nichole L King; Eric Deutsch; Jeffrey A Ranish; Alexey I Nesvizhskii; James S Eddes; Parag Mallick; Jimmy Eng; Frank Desiere; Mark R Flory; Daniel B Martin; Bong Kim; Hookeun Lee; Brian Raught; Ruedi Aebersold
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.
Genome biology 2006;7(11):R106.
2006: HUI ZHANG; Paul Loriaux; Jimmy Eng; David Campbell; Andrew Keller; Pat Moss; Richard Bonneau; Ning Zhang; Yong Zhou; Bernd Wollscheid; Kelly Cooke; Eugene C Yi; Hookeun Lee; Elaine Peskind; Jing Zhang; Richard D Smith; Ruedi Aebersold
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery.
Genome biology 2006;7(8):R73.
2006: Christopher Taylor; Henning Hermjakob; Randall K Julian; John S Garavelli; Ruedi Aebersold; Rolf Apweiler
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
Omics : a journal of integrative biology 2006;10(2):145-51.
2006: HUI ZHANG; Ruedi Aebersold
Isolation of glycoproteins and identification of their N-linked glycosylation sites.
Methods in molecular biology (Clifton, N.J.) 2006;328():177-85.
2006: Frank Desiere; Eric Deutsch; Nichole L King; Alexey I Nesvizhskii; Parag Mallick; Jimmy Eng; Sharon Chen; James S Eddes; Sandra N Loevenich; Ruedi Aebersold
The PeptideAtlas project.
Nucleic acids research 2006;34(Database issue):D655-8.
2005: Sharon Chen; Ruedi Aebersold
LC-MS solvent composition monitoring and chromatography alignment using mobile phase tracer molecules.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences 2005;829(1-2):107-14.
2005: Sandra Orchard; Henning Hermjakob; Chris Taylor; Ruedi Aebersold; Rolf Apweiler
Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative.
Proteomics 2005;5(18):4651-2.
2005: Manfred Heller; Mingliang Ye; Philippe E Michel; Patrick Morier; Daniel Stalder; Martin A Jünger; Ruedi Aebersold; Frédéric Reymond; Joël S Rossier
Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides.
Journal of proteome research 2005;4(6):2273-82.
2005: Sharon Chen; Eric Deutsch; Eugene C Yi; Xiao-jun Li; David R Goodlett; Ruedi Aebersold
Improving mass and liquid chromatography based identification of proteins using bayesian scoring.
Journal of proteome research 2005;4(6):2174-84.
2005: Ning Zhang; Xiao-jun Li; Mingliang Ye; Sheng Pan; Benno Schwikowski; Ruedi Aebersold
ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer.
Proteomics 2005;5(16):4096-106.
2005: Anne-Claude Gingras; Michael Caballero; Marcel Zarske; Amy Sanchez; Tony R Hazbun; Stanley Fields; Nahum Sonenberg; Ernst Hafen; Brian Raught; Ruedi Aebersold
A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity.
Molecular & cellular proteomics : MCP 2005;4(11):1725-40.
2005: Ru Chen; Eugene C Yi; Samuel Donohoe; Sheng Pan; Jimmy Eng; Kelly Cooke; David A Crispin; Zhaoli Lane; David R Goodlett; Mary P Bronner; Ruedi Aebersold; Teresa A Brentnall
Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape.
Gastroenterology 2005;129(4):1187-97.
2005: Judy L Shih; Samara Reck-Peterson; Rick Newitt; Mark S Mooseker; Ruedi Aebersold; Ira Herskowitz
Cell polarity protein Spa2P associates with proteins involved in actin function in Saccharomyces cerevisiae.
Molecular biology of the cell 2005;16(10):4595-608.
2005: Alexey I Nesvizhskii; Ruedi Aebersold
Interpretation of shotgun proteomic data: the protein inference problem.
Molecular & cellular proteomics : MCP 2005;4(10):1419-40.
2005: Marco Toigo; Samuel Donohoe; Gina Sperrazzo; Bradley Jarrold; Feng Wang; Richard Hinkle; Elizabeth Dolan; Robert J Isfort; Ruedi Aebersold
ICAT-MS-MS time course analysis of atrophying mouse skeletal muscle cytosolic subproteome.
Molecular bioSystems 2005;1(3):229-41.
2005: Ralph A Bradshaw; Al L Burlingame; Steve Carr; Ruedi Aebersold
Protein identification: the good, the bad, and the ugly.
Molecular & cellular proteomics : MCP 2005;4(9):1221-2.
2005: Xiao-jun Li; Eugene C Yi; Christopher J Kemp; HUI ZHANG; Ruedi Aebersold
A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry.
Molecular & cellular proteomics : MCP 2005;4(9):1328-40.
2005: W Andy Tao; Bernd Wollscheid; Robert O'Brien; Jimmy K Eng; Xiao-jun Li; Bernd Bodenmiller; Julian D Watts; Leroy Hood; Ruedi Aebersold
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry.
Nature methods 2005;2(8):591-8.
2005: Daniel B Martin; Jimmy K Eng; Alexey I Nesvizhskii; Andrew Gemmill; Ruedi Aebersold
Investigation of neutral loss during collision-induced dissociation of peptide ions.
Analytical chemistry 2005;77(15):4870-82.
2005: Eric Deutsch; Jimmy K Eng; HUI ZHANG; Nichole L King; Alexey I Nesvizhskii; Lin Biao; Hookeun Lee; Eugene C Yi; Reto Ossola; Ruedi Aebersold
Human Plasma PeptideAtlas.
Proteomics 2005;5(13):3497-500.
2005: Ruedi Aebersold; Leigh Anderson; Richard Caprioli; Brian J Druker; Leland H Hartwell; Richard Smith
Perspective: a program to improve protein biomarker discovery for cancer.
Journal of proteome research 2005;4(4):1104-9.
2005: Sabine P Schrimpf; Virginia Meskenaite; Erich Brunner; Dorothea Rutishauser; Pascal Walther; Jimmy Eng; Ruedi Aebersold; Peter Sonderegger
Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry.
Proteomics 2005;5(10):2531-41.
2005: Bernhard Kuster; Markus Schirle; Parag Mallick; Ruedi Aebersold
Scoring proteomes with proteotypic peptide probes.
Nature reviews. Molecular cell biology 2005;6(7):577-83.
2005: Jing Zhang; David R Goodlett; Joseph F Quinn; Elaine Peskind; Jeffrey A Kaye; Yong Zhou; Catherine Pan; Eugene Yi; Jimmy Eng; Qin Wang; Ruedi Aebersold; Thomas J Montine
Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease.
Journal of Alzheimer's disease : JAD 2005;7(2):125-33; discussion 173-80.
2005: Michael E Wright; David K Han; Ruedi Aebersold
Mass spectrometry-based expression profiling of clinical prostate cancer.
Molecular & cellular proteomics : MCP 2005;4(4):545-54.
2005: Ru Chen; Sheng Pan; Teresa A Brentnall; Ruedi Aebersold
Proteomic profiling of pancreatic cancer for biomarker discovery.
Molecular & cellular proteomics : MCP 2005;4(4):523-33.
2005: Anne-Claude Gingras; Ruedi Aebersold; Brian Raught
Advances in protein complex analysis using mass spectrometry.
The Journal of physiology 2005;563(Pt 1):11-21.
2005: Eugene C Yi; Xiao-Jun Li; Kelly Cooke; Hookeun Lee; Brian Raught; Andrew Page; Victoria Aneliunas; Philip Hieter; David R Goodlett; Ruedi Aebersold
Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme.
Proteomics 2005;5(2):380-7.
2005: Sheng Pan; HUI ZHANG; John Rush; Jimmy Eng; Ning Zhang; Dale Patterson; Michael J Comb; Ruedi Aebersold
High throughput proteome screening for biomarker detection.
Molecular & cellular proteomics : MCP 2005;4(2):182-90.
2005: HUI ZHANG; Eugene C Yi; Xiao-jun Li; Parag Mallick; Karen S Kelly-Spratt; Christophe Masselon; David G Camp; Richard D Smith; Christopher J Kemp; Ruedi Aebersold
High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry.
Molecular & cellular proteomics : MCP 2005;4(2):144-55.
2005: Jing Zhang; David R Goodlett; Elaine Peskind; Joseph F Quinn; Yong Zhou; Qin Wang; Catherine Pan; Eugene Yi; Jimmy Eng; Ruedi Aebersold; Thomas J Montine
Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid.
Neurobiology of aging 2005;26(2):207-27.
2005: Andrew Keller; Jimmy Eng; Ning Zhang; Xiao-jun Li; Ruedi Aebersold
A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
Molecular systems biology 2005;1():2005.0017.
2005: Garry L Corthals; Ruedi Aebersold; David R Goodlett
Identification of phosphorylation sites using microimmobilized metal affinity chromatography.
Methods in enzymology 2005;405():66-81.
2004: Marcello Marelli; Jennifer J Smith; Sunhee Jung; Eugene Yi; Alexey I Nesvizhskii; Rowan H Christmas; Ramsey A Saleem; Yuen Yi C Tam; Andrei Fagarasanu; David R Goodlett; Ruedi Aebersold; Richard A Rachubinski; John D Aitchison
Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane.
The Journal of cell biology 2004;167(6):1099-112.
2004: Xueyan Chen; Yong Chi; Andrew Bloecher; Ruedi Aebersold; Bruce E Clurman; James M Roberts
N-acetylation and ubiquitin-independent proteasomal degradation of p21(Cip1).
Molecular cell 2004;16(5):839-47.
2004: Wei-Chun Kao; Yet-Ran Chen; Eugene C Yi; Hookeun Lee; Qiang Tian; Keh-Ming Wu; Shih-Feng Tsai; Steve S-F Yu; Yu-Ju Chen; Ruedi Aebersold; Sunney I Chan
Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath).
The Journal of biological chemistry 2004;279(49):51554-60.
2004: Mark R Flory; Andrew R Carson; Eric G Muller; Ruedi Aebersold
An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome.
Molecular cell 2004;16(4):619-30.
2004: Patrick G A Pedrioli; Jimmy K Eng; Robert Hubley; Mathijs Vogelzang; Eric Deutsch; Brian Raught; Brian Pratt; Erik Nilsson; Ruth Hogue Angeletti; Rolf Apweiler; Kei Cheung; Catherine E Costello; Henning Hermjakob; Sequin Huang; Randall K Julian; Eugene Kapp; Mark E McComb; Stephen G Oliver; Gilbert S Omenn; Norman W Paton; Richard Simpson; Richard Smith; Christopher Taylor; Weimin Zhu; Ruedi Aebersold
A common open representation of mass spectrometry data and its application to proteomics research.
Nature biotechnology 2004;22(11):1459-66.
2004: Qiang Tian; Megan C Feetham; W Andy Tao; Xi C He; Linheng Li; Ruedi Aebersold; Leroy Hood
Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(43):15370-5.
2004: Kazuyuki Nakamura; Ruedi Aebersold; Amos Bairoch; Michael Dunn; Julio Celis; Samir Hanash; Denis Hochstrasser; Ian Humphrey-Smith; Peter James; Joachim Klose; Joshua LaBaer; Hanno Langen; Matthias Mann; Raj Parekh; Scott Patterson; Christopher Pearce; Peter Poepstorff; Richard J Simpson; Ian Tomlinson; Akira Tsugita; John Yates
[From genome to proteome--aim of human proteomics].
Seikagaku. The Journal of Japanese Biochemical Society 2004;76(10):1271-4.
2004: Wei Yan; Hookeun Lee; Eric Deutsch; Catherine Lazaro; Weiliang Tang; Eric Chen; Nelson Fausto; Michael G Katze; Ruedi Aebersold
A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry.
Molecular & cellular proteomics : MCP 2004;3(10):1039-41.
2004: Qiang Tian; Sergey B Stepaniants; Mao Mao; Lee Weng; Megan C Feetham; Michelle J Doyle; Eugene C Yi; Hongyue Dai; Vesteinn Thorsson; Jimmy Eng; David R Goodlett; Joel P Berger; Bert Gunter; Peter S Linseley; Roland B Stoughton; Ruedi Aebersold; Steven J Collins; William A Hanlon; Leroy Hood
Integrated genomic and proteomic analyses of gene expression in Mammalian cells.
Molecular & cellular proteomics : MCP 2004;3(10):960-9.
2004: Yong Zhou; Guangyu Gu; David R Goodlett; Terry Zhang; Catherine Pan; Thomas J Montine; Kathleen S Montine; Ruedi Aebersold; Jing Zhang
Analysis of alpha-synuclein-associated proteins by quantitative proteomics.
The Journal of biological chemistry 2004;279(37):39155-64.
2004: Eugenia Trushina; Roy B Dyer; John D Badger; Daren Ure; Lars Eide; David D Tran; Brent T Vrieze; Valerie Legendre-Guillemin; Peter S McPherson; Bhaskar S Mandavilli; Bennett Van Houten; Scott Zeitlin; Mark McNiven; Ruedi Aebersold; Michael Hayden; Joseph E Parisi; Erling Seeberg; Ioannis Dragatsis; Kelly Doyle; Anna Bender; Celin Chacko; Cynthia T McMurray
Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro.
Molecular and cellular biology 2004;24(18):8195-209.
2004: Yu Lu; Patricia Bottari; Frantisek Turecek; Ruedi Aebersold; Michael H Gelb
Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags.
Analytical chemistry 2004;76(14):4104-11.
2004: Xiao-jun Li; Patrick G A Pedrioli; Jimmy Eng; Dan Martin; Eugene C Yi; Hookeun Lee; Ruedi Aebersold
A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.
Analytical chemistry 2004;76(13):3856-60.
2004: Giuseppina Giglia-Mari; Frédéric Coin; Jeffrey A Ranish; Deborah Hoogstraten; Arjan F Theil; Nils Wijgers; Nicolaas G J Jaspers; Anja Raams; Manuela Argentini; Peter van der Spek; Elena Botta; Miria Stefanini; Jean-Marc Egly; Ruedi Aebersold; Jan H J Hoeijmakers; Wim Vermeulen
A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A.
Nature genetics 2004;36(7):714-9.
2004: Jeffrey A Ranish; Steven Hahn; Yu Lu; Eugene C Yi; Xiao-jun Li; Jimmy Eng; Ruedi Aebersold
Identification of TFB5, a new component of general transcription and DNA repair factor IIH.
Nature genetics 2004;36(7):707-13.
2004: Bernd Wollscheid; Julian D Watts; Ruedi Aebersold
Proteomics/genomics and signaling in lymphocytes.
Current opinion in immunology 2004;16(3):337-44.
2004: Steven Carr; Ruedi Aebersold; Michael Baldwin; Al L Burlingame; Karl Clauser; Alexey I Nesvizhskii
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.
Molecular & cellular proteomics : MCP 2004;3(6):531-3.
2004: Philip R Hardwidge; Isabel Rodriguez-Escudero; David Goode; Samuel Donohoe; Jimmy Eng; David R Goodlett; Ruedi Aebersold; B Brett Finlay
Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli.
The Journal of biological chemistry 2004;279(19):20127-36.
2004: Vivian L MacKay; Xiaohong Li; Mark R Flory; Eileen Turcott; G Lynn Law; Kyle A Serikawa; X L Xu; Hookeun Lee; David R Goodlett; Ruedi Aebersold; Lue Ping Zhao; David R Morris
Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone.
Molecular & cellular proteomics : MCP 2004;3(5):478-89.
2004: Hookeun Lee; Eugene C Yi; Bo Wen; Timothy P Reily; Lance Pohl; Sidney Nelson; Ruedi Aebersold; David R Goodlett
Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences 2004;803(1):101-10.
2004: Jennifer S Shumaker-Parry; Ruedi Aebersold; Charles T Campbell
Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy.
Analytical chemistry 2004;76(7):2071-82.
2004: Melanie L Mayer; Isabelle Pot; Michael Chang; Hong Xu; Victoria Aneliunas; Teresa Kwok; Rick Newitt; Ruedi Aebersold; Charles Boone; Grant W Brown; Philip Hieter
Identification of protein complexes required for efficient sister chromatid cohesion.
Molecular biology of the cell 2004;15(4):1736-45.
2004: Patricia Bottari; Ruedi Aebersold; Frantisek Turecek; Michael H Gelb
Design and synthesis of visible isotope-coded affinity tags for the absolute quantification of specific proteins in complex mixtures.
Bioconjugate chemistry 2004;15(2):380-8.
2004: Charis L Himeda; Jeffrey A Ranish; John C Angello; Pascal Maire; Ruedi Aebersold; Stephen D Hauschka
Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer.
Molecular and cellular biology 2004;24(5):2132-43.
2004: Margaret S Sozio; Meredith A Mathis; Jennifer A Young; Sébastien Wälchli; Lisa A Pitcher; Philip C Wrage; Beatrix Bartók; Amanda Campbell; Julian D Watts; Ruedi Aebersold; Rob Hooft van Huijsduijnen; Nicolai S C van Oers
PTPH1 is a predominant protein-tyrosine phosphatase capable of interacting with and dephosphorylating the T cell receptor zeta subunit.
The Journal of biological chemistry 2004;279(9):7760-9.
2004: Jennifer S Shumaker-Parry; M Hadi Zareie; Ruedi Aebersold; Charles T Campbell
Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy.
Analytical chemistry 2004;76(4):918-29.
2004: Alexey I Nesvizhskii; Ruedi Aebersold
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.
Drug discovery today 2004;9(4):173-81.
2004: HUI ZHANG; Wei Yan; Ruedi Aebersold
Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes.
Current opinion in chemical biology 2004;8(1):66-75.
2004: Margarita M Camacho Carvajal; Bernd Wollscheid; Ruedi Aebersold; Viktor Steimle; Wolfgang W A Schamel
Two-dimensional Blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates: a proteomics approach.
Molecular & cellular proteomics : MCP 2004;3(2):176-82.
2004: Bernd Wollscheid; Priska D von Haller; Eugene Yi; Samuel Donohoe; Kelly Vaughn; Andrew Keller; Alexey I Nesvizhskii; Jimmy Eng; Xiao-jun Li; David R Goodlett; Ruedi Aebersold; Julian D Watts
Lipid raft proteins and their identification in T lymphocytes.
Sub-cellular biochemistry 2004;37():121-52.
2004: Wei Yan; Hookeun Lee; Eugene C Yi; David J Reiss; Paul Shannon; Bartlomiej K Kwieciszewski; Carlos Coito; Xiao-jun Li; Andrew Keller; Jimmy Eng; Timothy Galitski; David R Goodlett; Ruedi Aebersold; Michael G Katze
System-based proteomic analysis of the interferon response in human liver cells.
Genome biology 2004;5(8):R54.
2004: Huilin Zhou; Rosemary Boyle; Ruedi Aebersold
Quantitative protein analysis by solid phase isotope tagging and mass spectrometry.
Methods in molecular biology (Clifton, N.J.) 2004;261():511-8.
2004: Daniel B Martin; David R Gifford; Michael E Wright; Andrew Keller; Eugene Yi; David R Goodlett; Ruedi Aebersold; Peter S Nelson
Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium.
Cancer research 2004;64(1):347-55.
2004: Marjorie Brand; Jeffrey A Ranish; Nicolas T Kummer; Joan Hamilton; Kazuhiko Igarashi; Claire Francastel; Tian H Chi; Gerald R Crabtree; Ruedi Aebersold; Mark Groudine
Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics.
Nature structural & molecular biology 2004;11(1):73-80.
2004: Frank Schmidt; Samuel Donahoe; Kristine Hagens; Jens Mattow; Ulrich E Schaible; Stefan H E Kaufmann; Ruedi Aebersold; Peter Jungblut
Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology.
Molecular & cellular proteomics : MCP 2004;3(1):24-42.
2003: Judith Haendeler; Guoyong Yin; Yukihiro Hojo; Yuji Saito; Matthew G Melaragno; Chen Yan; Virendra K Sharma; Manfred Heller; Ruedi Aebersold; Bradford C Berk
GIT1 mediates Src-dependent activation of phospholipase Cgamma by angiotensin II and epidermal growth factor.
The Journal of biological chemistry 2003;278(50):49936-44.
2003: Xiao-Jun Li; HUI ZHANG; Jeffrey A Ranish; Ruedi Aebersold
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry.
Analytical chemistry 2003;75(23):6648-57.
2003: Alexey I Nesvizhskii; Andrew Keller; Eugene Kolker; Ruedi Aebersold
A statistical model for identifying proteins by tandem mass spectrometry.
Analytical chemistry 2003;75(17):4646-58.
2003: Michael E Wright; Ming-Jer Tsai; Ruedi Aebersold
Androgen receptor represses the neuroendocrine transdifferentiation process in prostate cancer cells.
Molecular endocrinology (Baltimore, Md.) 2003;17(9):1726-37.
2003: Young Ah Goo; Eugene C Yi; Nitin S Baliga; Weiguo A Tao; Min Pan; Ruedi Aebersold; David R Goodlett; Leroy Hood; Wailap Victor Ng
Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1.
Molecular & cellular proteomics : MCP 2003;2(8):506-24.
2003: Shen Hu; Zhang Le; Richard Newitt; Ruedi Aebersold; James R Kraly; Megan Jones; Norman J Dovichi
Identification of proteins in single-cell capillary electrophoresis fingerprints based on comigration with standard proteins.
Analytical chemistry 2003;75(14):3502-5.
2003: Tina Guina; Manhong Wu; Samuel I Miller; Samuel O Purvine; Eugene C Yi; Jimmy Eng; David R Goodlett; Ruedi Aebersold; Robert Ernst; Kimberly A Lee
Proteomic analysis of Pseudomonas aeruginosa grown under magnesium limitation.
Journal of the American Society for Mass Spectrometry 2003;14(7):742-51.
2003: Yuzuru Shiio; Robert N Eisenman; Eugene C Yi; Samuel Donohoe; David R Goodlett; Ruedi Aebersold
Quantitative proteomic analysis of chromatin-associated factors.
Journal of the American Society for Mass Spectrometry 2003;14(7):696-703.
2003: Ruedi Aebersold
A mass spectrometric journey into protein and proteome research.
Journal of the American Society for Mass Spectrometry 2003;14(7):685-95.
2003: Priska D von Haller; Eugene Yi; Samuel Donohoe; Kelly Vaughn; Andrew Keller; Alexey I Nesvizhskii; Jimmy Eng; Xiao-jun Li; David R Goodlett; Ruedi Aebersold; Julian D Watts
The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation.
Molecular & cellular proteomics : MCP 2003;2(7):428-42.
2003: Priska D von Haller; Eugene Yi; Samuel Donohoe; Kelly Vaughn; Andrew Keller; Alexey I Nesvizhskii; Jimmy Eng; Xiao-jun Li; David R Goodlett; Ruedi Aebersold; Julian D Watts
The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts.
Molecular & cellular proteomics : MCP 2003;2(7):426-7.
2003: Ruedi Aebersold
Quantitative proteome analysis: methods and applications.
The Journal of infectious diseases 2003;187 Suppl 2():S315-20.
2003: HUI ZHANG; Xiao-Jun Li; Daniel B Martin; Ruedi Aebersold
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry.
Nature biotechnology 2003;21(6):660-6.
2003: Robert J Seward; Priska D von Haller; Ruedi Aebersold; Brigitte T Huber
Phosphorylation of the pro-apoptotic protein Bim in lymphocytes is associated with protection from apoptosis.
Molecular immunology 2003;39(16):983-93.
2003: Kenichi Chikamori; Dale R Grabowski; Michael Kinter; Belinda B Willard; Satya Yadav; Ruedi Aebersold; Ronald M Bukowski; Ian D Hickson; Anni H Andersen; Ram Ganapathi; Mahrukh K Ganapathi
Phosphorylation of serine 1106 in the catalytic domain of topoisomerase II alpha regulates enzymatic activity and drug sensitivity.
The Journal of biological chemistry 2003;278(15):12696-702.
2003: Seon-Ah Ha; Javad Torabinejad; Daryll B DeWald; Markus R Wenk; Louise Lucast; Pietro De Camilli; Richard A Newitt; Ruedi Aebersold; Steven F Nothwehr
The synaptojanin-like protein Inp53/Sjl3 functions with clathrin in a yeast TGN-to-endosome pathway distinct from the GGA protein-dependent pathway.
Molecular biology of the cell 2003;14(4):1319-33.
2003: Ruedi Aebersold; Matthias Mann
Mass spectrometry-based proteomics.
Nature 2003;422(6928):198-207.
2003: Ruedi Aebersold
Constellations in a cellular universe.
Nature 2003;422(6928):115-6.
2003: Tina Guina; Samuel O Purvine; Eugene C Yi; Jimmy Eng; David R Goodlett; Ruedi Aebersold; Samuel I Miller
Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(5):2771-6.
2003: Christopher Taylor; Norman W Paton; Kevin L Garwood; Paul D Kirby; David Stead; Zhikang Yin; Eric Deutsch; Laura Selway; Janet Walker; Isabel Riba; shabaz mohammed; Michael J Deery; Julie A Howard; Tom P J Dunkley; Ruedi Aebersold; Douglas B Kell; Kathryn S Lilley; Peter Roepstorff; John R Yates; Andrew Brass; Alistair J P Brown; Phillip Cash; Simon J Gaskell; Simon Hubbard; Stephen G Oliver
A systematic approach to modeling, capturing, and disseminating proteomics experimental data.
Nature biotechnology 2003;21(3):247-54.
2003: Scott D Patterson; Ruedi Aebersold
Proteomics: the first decade and beyond.
Nature genetics 2003;33 Suppl():311-23.
2003: Jeffrey A Ranish; Eugene C Yi; Deena M Leslie; Samuel O Purvine; David R Goodlett; Jimmy Eng; Ruedi Aebersold
The study of macromolecular complexes by quantitative proteomics.
Nature genetics 2003;33(3):349-55.
2003: Timothy J Griffin; Chris M Lock; Xiao-jun Li; Alpesh Patel; Iryna Chervetsova; Hookeun Lee; Michael E Wright; Jeffrey A Ranish; Sharon Chen; Ruedi Aebersold
Abundance ratio-dependent proteomic analysis by mass spectrometry.
Analytical chemistry 2003;75(4):867-74.
2003: W Andy Tao; Ruedi Aebersold
Advances in quantitative proteomics via stable isotope tagging and mass spectrometry.
Current opinion in biotechnology 2003;14(1):110-8.
2003: Michael E Wright; Jimmy Eng; James Sherman; David M Hockenbery; Peter S Nelson; Timothy Galitski; Ruedi Aebersold
Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.
Genome biology 2003;5(1):R4.
2003: Mark R Flory; Ruedi Aebersold
Proteomic approaches for the identification of cell cycle-related drug targets.
Progress in cell cycle research 2003;5():167-71.
2003: Eugene C Yi; Hookeun Lee; Ruedi Aebersold; David R Goodlett
A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation.
Rapid communications in mass spectrometry : RCM 2003;17(18):2093-8.
2002: Mark R Flory; Timothy J Griffin; Daniel Martin; Ruedi Aebersold
Advances in quantitative proteomics using stable isotope tags.
Trends in biotechnology 2002;20(12 Suppl):S23-9.
2002: Ruedi Aebersold; Benjamin F Cravatt
Proteomics--advances, applications and the challenges that remain.
Trends in biotechnology 2002;20(12 Suppl):S1-2.
2002: Nitin S Baliga; Min Pan; Young Ah Goo; Eugene C Yi; David R Goodlett; Krassen Dimitrov; Paul Shannon; Ruedi Aebersold; Wailap Victor Ng; Leroy Hood
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(23):14913-8.
2002: Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
Analytical chemistry 2002;74(20):5383-92.
2002: Ning Zhang; Ruedi Aebersold; Benno Schwikowski
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data.
Proteomics 2002;2(10):1406-12.
2002: Yuzuru Shiio; Samuel Donohoe; Eugene C Yi; David R Goodlett; Ruedi Aebersold; Robert N Eisenman
Quantitative proteomic analysis of Myc oncoprotein function.
The EMBO journal 2002;21(19):5088-96.
2002: Eugene C Yi; Marcello Marelli; Hookeun Lee; Samuel O Purvine; Ruedi Aebersold; John D Aitchison; David R Goodlett
Approaching complete peroxisome characterization by gas-phase fractionation.
Electrophoresis 2002;23(18):3205-16.
2002: Hookeun Lee; Timothy J Griffin; Steven P Gygi; Beate Rist; Ruedi Aebersold
Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis.
Analytical chemistry 2002;74(17):4353-60.
2002: Tong Yang; Peter J Espenshade; Michael E Wright; Yabe Daisuke; Yi Gong; Ruedi Aebersold; Joseph L Goldstein; Michael S Brown
Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER.
Cell 2002;110(4):489-500.
2002: Ruedi Aebersold; Julian D Watts
The need for national centers for proteomics.
Nature biotechnology 2002;20(7):651.
2002: Thierry Rabilloud; Manfred Heller; Francoise Gasnier; Sylvie Luche; Catherine Rey; Ruedi Aebersold; Mohamed Benahmed; Pierre Louisot; Joël Lunardi
Proteomics analysis of cellular response to oxidative stress. Evidence for in vivo overoxidation of peroxiredoxins at their active site.
The Journal of biological chemistry 2002;277(22):19396-401.
2002: Eric A James; Steven P Gygi; Michael L Adams; Robert H Pierce; Nelson Fausto; Ruedi Aebersold; Sidney D Nelson; Sam A Bruschi
Mitochondrial aconitase modification, functional inhibition, and evidence for a supramolecular complex of the TCA cycle by the renal toxicant S-(1,1,2,2-tetrafluoroethyl)-L-cysteine.
Biochemistry 2002;41(21):6789-97.
2002: Huilin Zhou; Jeffrey A Ranish; Julian D Watts; Ruedi Aebersold
Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry.
Nature biotechnology 2002;20(5):512-5.
2002: Louis A Marotti; Rick Newitt; Yuqi Wang; Ruedi Aebersold; Henrik G Dohlman
Direct identification of a G protein ubiquitination site by mass spectrometry.
Biochemistry 2002;41(16):5067-74.
2002: Timothy J Griffin; Steven P Gygi; Trey Ideker; Beate Rist; Jimmy Eng; Leroy Hood; Ruedi Aebersold
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae.
Molecular & cellular proteomics : MCP 2002;1(4):323-33.
2002: Shara Kabak; Brian J Skaggs; Michael R Gold; Michael Affolter; Kelly L West; Mark S Foster; Karyn F Siemasko; Andrew C Chan; Ruedi Aebersold; Marcus R Clark
The direct recruitment of BLNK to immunoglobulin alpha couples the B-cell antigen receptor to distal signaling pathways.
Molecular and cellular biology 2002;22(8):2524-35.
2002: Jessica A Hamerman; Fumitaka Hayashi; Lea A Schroeder; Steven P Gygi; Arthur L Haas; Lynne Hampson; Paul B Coughlin; Ruedi Aebersold; Alan Aderem
Serpin 2a is induced in activated macrophages and conjugates to a ubiquitin homolog.
Journal of immunology (Baltimore, Md. : 1950) 2002;168(5):2415-23.
2002: Shaynoor Dramsi; Michael P Scheid; Arpita Maiti; Payman Hojabrpour; Xianming Chen; Kathryn Schubert; David R Goodlett; Ruedi Aebersold; Vincent Duronio
Identification of a novel phosphorylation site, Ser-170, as a regulator of bad pro-apoptotic activity.
The Journal of biological chemistry 2002;277(8):6399-405.
2002: Steven P Gygi; Beate Rist; Timothy J Griffin; Jimmy Eng; Ruedi Aebersold
Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags.
Journal of proteome research 2002;1(1):47-54.
2002: Marcus Smolka; Huilin Zhou; Ruedi Aebersold
Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry.
Molecular & cellular proteomics : MCP 2002;1(1):19-29.
2001: Timothy J Griffin; Ruedi Aebersold
Advances in proteome analysis by mass spectrometry.
The Journal of biological chemistry 2001;276(49):45497-500.
2001: Timothy J Griffin; D K Han; Steven P Gygi; Beate Rist; Hookeun Lee; Ruedi Aebersold; K C Parker
Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry.
Journal of the American Society for Mass Spectrometry 2001;12(12):1238-46.
2001: Thierry Rabilloud; M Heller; Maria Pia Rigobello; Alberto Bindoli; Ruedi Aebersold; Joël Lunardi
The mitochondrial antioxidant defence system and its response to oxidative stress.
Proteomics 2001;1(9):1105-10.
2001: Priska D von Haller; Samuel Donohoe; David R Goodlett; Ruedi Aebersold; Julian D Watts
Mass spectrometric characterization of proteins extracted from Jurkat T cell detergent-resistant membrane domains.
Proteomics 2001;1(8):1010-21.
2001: Trey Ideker; Vesteinn Thorsson; Jeffrey A Ranish; Rowan H Christmas; J Buhler; Jimmy K Eng; Roger Bumgarner; David R Goodlett; Ruedi Aebersold; Leroy Hood
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
Science (New York, N.Y.) 2001;292(5518):929-34.
2001: H Zhou; Julian D Watts; Ruedi Aebersold
A systematic approach to the analysis of protein phosphorylation.
Nature biotechnology 2001;19(4):375-8.
2001: Y Liu; Jeffrey A Ranish; Ruedi Aebersold; Steven Hahn
Yeast nuclear extract contains two major forms of RNA polymerase II mediator complexes.
The Journal of biological chemistry 2001;276(10):7169-75.
2001: Timothy J Griffin; Steven P Gygi; Beate Rist; Ruedi Aebersold; Alexander Loboda; A Jilkine; Werner Ens; Kenneth G Standing
Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer.
Analytical chemistry 2001;73(5):978-86.
2001: M Heller; Julian D Watts; Ruedi Aebersold
CD28 stimulation regulates its association with N-ethylmaleimide-sensitive fusion protein and other proteins involved in vesicle sorting.
Proteomics 2001;1(1):70-8.
2001: David R Goodlett; Andrew Keller; Julian D Watts; R Newitt; Eugene C Yi; Samuel O Purvine; Jimmy K Eng; Priska D von Haller; Ruedi Aebersold; Eugene Kolker
Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.
Rapid communications in mass spectrometry : RCM 2001;15(14):1214-21.
2000: Michael G Katze; Bartlomiej K Kwieciszewski; D R Goodlett; Collin M Blakely; Petra Neddermann; Seng-Lai Tan; Ruedi Aebersold
Ser(2194) is a highly conserved major phosphorylation site of the hepatitis C virus nonstructural protein NS5A.
Virology 2000;278(2):501-13.
2000: D L Morrison; A Yee; Harry Paddon; D Vilimek; Ruedi Aebersold; Steven Pelech
Regulation of the meiosis-inhibited protein kinase, a p38(MAPK) isoform, during meiosis and following fertilization of seastar oocytes.
The Journal of biological chemistry 2000;275(44):34236-44.
2000: P A Haynes; Ruedi Aebersold
Simultaneous detection and identification of O-GlcNAc-modified glycoproteins using liquid chromatography-tandem mass spectrometry.
Analytical chemistry 2000;72(21):5402-10.
2000: Steven P Gygi; Ruedi Aebersold
Mass spectrometry and proteomics.
Current opinion in chemical biology 2000;4(5):489-94.
2000: Andrei M Mikheev; S A Mikheev; Y Zhang; Ruedi Aebersold; Helmut Zarbl
CArG binding factor A (CBF-A) is involved in transcriptional regulation of the rat Ha-ras promoter.
Nucleic acids research 2000;28(19):3762-70.
2000: Steven P Gygi; Garry L Corthals; Y Zhang; YP Rochon; Ruedi Aebersold
Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(17):9390-5.
2000: Steven P Gygi; Beate Rist; Ruedi Aebersold
Measuring gene expression by quantitative proteome analysis.
Current opinion in biotechnology 2000;11(4):396-401.
2000: M Heller; David R Goodlett; Julian D Watts; Ruedi Aebersold
A comprehensive characterization of the T-cell antigen receptor complex composition by microcapillary liquid chromatography-tandem mass spectrometry.
Electrophoresis 2000;21(11):2180-95.
2000: I Ebrini; D Agnello; Ingrid Miller; Pia Villa; Maddalena Fratelli; Pietro Ghezzi; Manfred Gemeiner; J Chan; Ruedi Aebersold; Elisabetta Gianazza
Proteins of rat serum V: adjuvant arthritis and its modulation by nonsteroidal anti-inflammatory drugs.
Electrophoresis 2000;21(11):2170-9.
2000: P S Nelson; D Han; YP Rochon; Garry L Corthals; Lin Biao; A Monson; V Nguyen; B R Franza; S R Plymate; Ruedi Aebersold; L Hood
Comprehensive analyses of prostate gene expression: convergence of expressed sequence tag databases, transcript profiling and proteomics.
Electrophoresis 2000;21(9):1823-31.
2000: Ruedi Aebersold; Leroy Hood; Julian D Watts
Equipping scientists for the new biology.
Nature biotechnology 2000;18(4):359.
2000: David R Goodlett; James E Bruce; Gordon A Anderson; Beate Rist; Ljiljana Pasa-Tolic; O Fiehn; Richard D Smith; Ruedi Aebersold
Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching.
Analytical chemistry 2000;72(6):1112-8.
2000: Jerzy Ostrowski; Daniel S Schullery; Oleg Denisenko; Yuji Higaki; J Watts; Ruedi Aebersold; Luise Stempka; Michael Gschwendt; Karol Bomsztyk
Role of tyrosine phosphorylation in the regulation of the interaction of heterogenous nuclear ribonucleoprotein K protein with its protein and RNA partners.
The Journal of biological chemistry 2000;275(5):3619-28.
2000: Ruedi Aebersold; Beate Rist; Steven P Gygi
Quantitative proteome analysis: methods and applications.
Annals of the New York Academy of Sciences 2000;919():33-47.
2000: David R Goodlett; Ruedi Aebersold; Julian D Watts
Quantitative in vitro kinase reaction as a guide for phosphoprotein analysis by mass spectrometry.
Rapid communications in mass spectrometry : RCM 2000;14(5):344-8.
1999: Tiffany garrison; Yalan Zhang; MH Pausch; Donald M Apanovitch; Ruedi Aebersold; Henrik G Dohlman
Feedback phosphorylation of an RGS protein by MAP kinase in yeast.
The Journal of biological chemistry 1999;274(51):36387-91.
1999: Thierry Rabilloud; Thierry Blisnick; M Heller; Sylvie Luche; Ruedi Aebersold; Joël Lunardi; Catherine Braun Breton
Analysis of membrane proteins by two-dimensional electrophoresis: comparison of the proteins extracted from normal or Plasmodium falciparum-infected erythrocyte ghosts.
Electrophoresis 1999;20(18):3603-10.
1999: Ivano Eberini; Ingrid Miller; Manfred Gemeiner; PA Haynes; Ruedi Aebersold; Lina Puglisi; C R Sirtori; Elisabetta Gianazza
A web site for the rat serum protein study group.
Electrophoresis 1999;20(18):3599-602.
1999: L A Charlton; Mohamed Sayed; I Clark-Lewis; Ruedi Aebersold; Steven Pelech
Characterization of an activated ribosomal S6 kinase variant from maturing sea star oocytes: association with phosphatase 2A and substrate specificity.
Journal of cellular biochemistry 1999;75(2):310-26.
1999: J H Chan; A T Timperman; D Qin; Ruedi Aebersold
Microfabricated polymer devices for automated sample delivery of peptides for analysis by electrospray ionization tandem mass spectrometry.
Analytical chemistry 1999;71(20):4437-44.
1999: Byron Gallis; Garry L Corthals; David R Goodlett; H Ueba; Francis Kim; S R Presnell; D Figeys; David G Harrison; Bradford C Berk; Ruedi Aebersold; Marshall A Corson
Identification of flow-dependent endothelial nitric-oxide synthase phosphorylation sites by mass spectrometry and regulation of phosphorylation and nitric oxide production by the phosphatidylinositol 3-kinase inhibitor LY294002.
The Journal of biological chemistry 1999;274(42):30101-8.
1999: Steven P Gygi; Beate Rist; SA Gerber; Frantisek Turecek; Michael H Gelb; Ruedi Aebersold
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
Nature biotechnology 1999;17(10):994-9.
1999: D Figeys; Garry L Corthals; Byron Gallis; David R Goodlett; A Ducret; Marshall A Corson; Ruedi Aebersold
Data-dependent modulation of solid-phase extraction capillary electrophoresis for the analysis of complex peptide and phosphopeptide mixtures by tandem mass spectrometry: application to endothelial nitric oxide synthase.
Analytical chemistry 1999;71(13):2279-87.
1999: Julian D Watts; Ruedi Aebersold; AJ Polverino; SD Patterson; M Gu
Ceramide second messengers and ceramide assays.
Trends in biochemical sciences 1999;24(6):228.
1999: H Yokota; K Fung; Barbara J Trask; Ger van den Engh; Mehmet Sarikaya; Ruedi Aebersold
Sharp DNA bends as landmarks of protein-binding sites on straightened DNA.
Analytical chemistry 1999;71(9):1663-7.
1999: Ingrid Miller; PA Haynes; Ivano Eberini; Manfred Gemeiner; Ruedi Aebersold; Elisabetta Gianazza
Proteins of rat serum: III. Gender-related differences in protein concentration under baseline conditions and upon experimental inflammation as evaluated by two-dimensional electrophoresis.
Electrophoresis 1999;20(4-5):836-45.
1999: Steven P Gygi; YP Rochon; B R Franza; Ruedi Aebersold
Correlation between protein and mRNA abundance in yeast.
Molecular and cellular biology 1999;19(3):1720-30.
1999: Julian D Watts; M Gu; SD Patterson; Ruedi Aebersold; AJ Polverino
On the complexities of ceramide changes in cells undergoing apoptosis: lack of evidence for a second messenger function in apoptotic induction.
Cell death and differentiation 1999;6(2):105-14.
1999: SP Gygi; David K Han; Anne-Claude Gingras; N Sonenberg; Ruedi Aebersold
Protein analysis by mass spectrometry and sequence database searching: tools for cancer research in the post-genomic era.
Electrophoresis 1999;20(2):310-9.
1999: Steven P Gygi; Ruedi Aebersold
Absolute quantitation of 2-D protein spots.
Methods in molecular biology (Clifton, N.J.) 1999;112():417-21.
1998: A Ducret; N Bartone; P A Haynes; A Blanchard; Ruedi Aebersold
A simplified gradient solvent delivery system for capillary liquid chromatography-electrospray ionization mass spectrometry.
Analytical biochemistry 1998;265(1):129-38.
1998: H Yokota; D A Nickerson; Barbara J Trask; Ger van den Engh; Martin Hirst; Ivan Sadowski; Ruedi Aebersold
Mapping a protein-binding site on straightened DNA by atomic force microscopy.
Analytical biochemistry 1998;264(2):158-64.
1998: Jin Wang; A Ducret; Yaping Tu; Tohru Kozasa; Ruedi Aebersold; Elliott M Ross
RGSZ1, a Gz-selective RGS protein in brain. Structure, membrane association, regulation by Galphaz phosphorylation, and relationship to a Gz gtpase-activating protein subfamily.
The Journal of biological chemistry 1998;273(40):26014-25.
1998: D Figeys; Y Zhang; Ruedi Aebersold
Optimization of solid phase microextraction - capillary zone electrophoresis - mass spectrometry for high sensitivity protein identification.
Electrophoresis 1998;19(13):2338-47.
1998: D Figeys; Steven P Gygi; G McKinnon; Ruedi Aebersold
An integrated microfluidics-tandem mass spectrometry system for automated protein analysis.
Analytical chemistry 1998;70(18):3728-34.
1998: D Figeys; Ruedi Aebersold
Nanoflow solvent gradient delivery from a microfabricated device for protein identifications by electrospray ionization mass spectrometry.
Analytical chemistry 1998;70(18):3721-7.
1998: PA Haynes; SP Gygi; D Figeys; Ruedi Aebersold
Proteome analysis: biological assay or data archive?
Electrophoresis 1998;19(11):1862-71.
1998: Ruedi Aebersold; D Figeys; Steven P Gygi; Garry L Corthals; P Haynes; Beate Rist; J Sherman; Y Zhang; David R Goodlett
Towards an integrated analytical technology for the generation of multidimensional protein expression maps.
Journal of protein chemistry 1998;17(6):533-5.
1998: Y Zhang; D Figeys; Ruedi Aebersold
Purification of trypsin for mass spectrometric identification of proteins at high sensitivity.
Analytical biochemistry 1998;261(1):124-7.
1998: D Figeys; SP Gygi; Y Zhang; J Watts; M Gu; Ruedi Aebersold
Electrophoresis combined with novel mass spectrometry techniques: powerful tools for the analysis of proteins and proteomes.
Electrophoresis 1998;19(10):1811-8.
1998: Ingrid Miller; PA Haynes; Manfred Gemeiner; Ruedi Aebersold; C Manzoni; Maria Rosa Lovati; M Vignati; Ivano Eberini; Elisabetta Gianazza
Proteins of rat serum: II. Influence of some biological parameters of the two-dimensional electrophoresis pattern.
Electrophoresis 1998;19(8-9):1493-500.
1998: PA Haynes; Ingrid Miller; Ruedi Aebersold; Manfred Gemeiner; Ivano Eberini; Maria Rosa Lovati; C Manzoni; M Vignati; Elisabetta Gianazza
Proteins of rat serum: I. Establishing a reference two-dimensional electrophoresis map by immunodetection and microbore high performance liquid chromatography-electrospray mass spectrometry.
Electrophoresis 1998;19(8-9):1484-92.
1998: PA Haynes; N Fripp; Ruedi Aebersold
Identification of gel-separated proteins by liquid chromatography-electrospray tandem mass spectrometry: comparison of methods and their limitations.
Electrophoresis 1998;19(6):939-45.
1998: D Figeys; Ruedi Aebersold
High sensitivity analysis of proteins and peptides by capillary electrophoresis-tandem mass spectrometry: recent developments in technology and applications.
Electrophoresis 1998;19(6):885-92.
1998: Armin Steinmetz; Marcela Hermann; Johannes Nimpf; Ruedi Aebersold; A Ducret; Richard B Weinberg; Wolfgang J Schneider
Expression and conservation of apolipoprotein AIV in an avian species.
The Journal of biological chemistry 1998;273(17):10543-9.
1998: A Ducret; I Van Oostveen; Jimmy K Eng; John R Yates; Ruedi Aebersold
High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry.
Protein science : a publication of the Protein Society 1998;7(3):706-19.
1997: D Figeys; Y Ning; Ruedi Aebersold
A microfabricated device for rapid protein identification by microelectrospray ion trap mass spectrometry.
Analytical chemistry 1997;69(16):3153-60.
1997: D Figeys; Ruedi Aebersold
Capillary electrophoresis of peptides and proteins at neutral pH in capillaries covalently coated with polyethyleneimine.
Journal of chromatography. B, Biomedical sciences and applications 1997;695(1):163-8.
1997: Julian D Watts; M Gu; AJ Polverino; SD Patterson; Ruedi Aebersold
Fas-induced apoptosis of T cells occurs independently of ceramide generation.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(14):7292-6.
1997: A Ducret; E J Bures; Ruedi Aebersold
High-sensitivity detection of 4-(3-pyridinylmethylaminocarboxypropyl) phenylthiohydantoins by capillary liquid chromatography-microelectrospray ion trap mass spectrometry.
Journal of protein chemistry 1997;16(5):323-8.
1997: I van Oostveen; A Ducret; Ruedi Aebersold
Colloidal silver staining of electroblotted proteins for high sensitivity peptide mapping by liquid chromatography-electrospray ionization tandem mass spectrometry.
Analytical biochemistry 1997;247(2):310-8.
1997: C K Palaty; G Kalmar; Georgia Tai; S Oh; L Amankawa; M Affolter; Ruedi Aebersold; Steven Pelech
Identification of the autophosphorylation sites of the Xenopus laevis Pim-1 proto-oncogene-encoded protein kinase.
The Journal of biological chemistry 1997;272(16):10514-21.
1997: D Figeys; Ruedi Aebersold
High sensitivity identification of proteins by electrospray ionization tandem mass spectrometry: initial comparison between an ion trap mass spectrometer and a triple quadrupole mass spectrometer.
Electrophoresis 1997;18(3-4):360-8.
1997: D Figeys; A Ducret; Ruedi Aebersold
Identification of proteins by capillary electrophoresis-tandem mass spectrometry. Evaluation of an on-line solid-phase extraction device.
Journal of chromatography. A 1997;763(1-2):295-306.
1997: M Gu; JL Kerwin; Julian D Watts; Ruedi Aebersold
Ceramide profiling of complex lipid mixtures by electrospray ionization mass spectrometry.
Analytical biochemistry 1997;244(2):347-56.
1996: J La Roche; G W van der Staay; Frédéric Partensky; A Ducret; Ruedi Aebersold; R Li; S S Golden; R G Hiller; P M Wrench; A W Larkum; Beverley R Green
Independent evolution of the prochlorophyte and green plant chlorophyll a/b light-harvesting proteins.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(26):15244-8.
1996: D G Durnford; Ruedi Aebersold; Beverley R Green
The fucoxanthin-chlorophyll proteins from a chromophyte alga are part of a large multigene family: structural and evolutionary relationships to other light harvesting antennae.
Molecular & general genetics : MGG 1996;253(3):377-86.
1996: Julian D Watts; Thea Brabb; E J Bures; R L Wange; Lawrence E Samelson; Ruedi Aebersold
Identification and characterization of a substrate specific for the T cell protein tyrosine kinase ZAP-70.
FEBS letters 1996;398(2-3):217-22.
1996: D Figeys; A Ducret; John R Yates; Ruedi Aebersold
Protein identification by solid phase microextraction-capillary zone electrophoresis-microelectrospray-tandem mass spectrometry.
Nature biotechnology 1996;14(11):1579-83.
1996: Heung-Chin Cheng; Jeffrey D Bjorge; Ruedi Aebersold; Donald J Fujita; J H Wang
Purification of bovine thymus cytosolic C-terminal Src kinase (CSK) and demonstration of differential efficiencies of phosphorylation and inactivation of p56lyn and pp60c-src by CSK.
Biochemistry 1996;35(36):11874-87.
1996: N Isakov; R L Wange; Julian D Watts; Ruedi Aebersold; Lawrence E Samelson
Purification and characterization of human ZAP-70 protein-tyrosine kinase from a baculovirus expression system.
The Journal of biological chemistry 1996;271(26):15753-61.
1996: D Figeys; I van Oostveen; A Ducret; Ruedi Aebersold
Protein identification by capillary zone electrophoresis/microelectrospray ionization-tandem mass spectrometry at the subfemtomole level.
Analytical chemistry 1996;68(11):1822-8.
1996: S G Whalen; Anne-Claude Gingras; L Amankwa; Sylvie Mader; Philip E Branton; Ruedi Aebersold; Nahum Sonenberg
Phosphorylation of eIF-4E on serine 209 by protein kinase C is inhibited by the translational repressors, 4E-binding proteins.
The Journal of biological chemistry 1996;271(20):11831-7.
1996: A Ducret; C F Bruun; E J Bures; G Marhaug; Gunnar Husby; Ruedi Aebersold
Characterization of human serum amyloid A protein isoforms separated by two-dimensional electrophoresis by liquid chromatography/electrospray ionization tandem mass spectrometry.
Electrophoresis 1996;17(5):866-76.
1996: D Tull; D L Burgoyne; DT Chow; Stephen G Withers; Ruedi Aebersold
A mass spectrometry-based approach for probing enzyme active sites: identification of Glu 127 in Cellulomonas fimi exoglycanase as the residue modified by N-bromoacetyl cellobiosylamine.
Analytical biochemistry 1996;234(2):119-25.
1996: D H Ng; Julian D Watts; Ruedi Aebersold; Pauline Johnson
Demonstration of a direct interaction between p56lck and the cytoplasmic domain of CD45 in vitro.
The Journal of biological chemistry 1996;271(3):1295-300.
1995: J C Gebler; D E Trimbur; A J Warren; Ruedi Aebersold; M Namchuk; Stephen G Withers
Substrate-induced inactivation of a crippled beta-glucosidase mutant: identification of the labeled amino acid and mutagenic analysis of its role.
Biochemistry 1995;34(44):14547-53.
1995: R L Wange; R Guitián; N Isakov; Julian D Watts; Ruedi Aebersold; Lawrence E Samelson
Activating and inhibitory mutations in adjacent tyrosines in the kinase domain of ZAP-70.
The Journal of biological chemistry 1995;270(32):18730-3.
1995: Ute Dechert; M Affolter; K W Harder; J Matthews; P Owen; Ian Clark-Lewis; M L Thomas; Ruedi Aebersold; Frank R Jirik
Comparison of the specificity of bacterially expressed cytoplasmic protein-tyrosine phosphatases SHP and SH-PTP2 towards synthetic phosphopeptide substrates.
European journal of biochemistry / FEBS 1995;231(3):673-81.
1995: Stephen G Withers; Ruedi Aebersold
Approaches to labeling and identification of active site residues in glycosidases.
Protein science : a publication of the Protein Society 1995;4(3):361-72.
1995: D Tull; S Miao; Stephen G Withers; Ruedi Aebersold
Identification of derivatized peptides without radiolabels: tandem mass spectrometric localization of the tagged active-site nucleophiles of two cellulases and a beta-glucosidase.
Analytical biochemistry 1995;224(2):509-14.
1995: R L Wange; N Isakov; T R Burke; A Otaka; P P Roller; Julian D Watts; Ruedi Aebersold; Lawrence E Samelson
F2(Pmp)2-TAM zeta 3, a novel competitive inhibitor of the binding of ZAP-70 to the T cell antigen receptor, blocks early T cell signaling.
The Journal of biological chemistry 1995;270(2):944-8.
1995: daniel Hess; H Nika; DT Chow; E J Bures; H D Morrison; Ruedi Aebersold
Liquid chromatography-electrospray ionization mass spectrometry of 4-(3-pyridinylmethylaminocarboxypropyl) phenylthiohydantoins.
Analytical biochemistry 1995;224(1):373-81.
1995: E J Bures; H Nika; DT Chow; H D Morrison; daniel Hess; Ruedi Aebersold
Synthesis of the protein-sequencing reagent 4-(3-pyridinylmethylaminocarboxypropyl) phenyl isothiocyanate and characterization of 4-(3-pyridinylmethylaminocarboxypropyl) phenylthiohydantoins.
Analytical biochemistry 1995;224(1):364-72.
1995: L N Amankwa; K Harder; Frank R Jirik; Ruedi Aebersold
High-sensitivity determination of tyrosine-phosphorylated peptides by on-line enzyme reactor and electrospray ionization mass spectrometry.
Protein science : a publication of the Protein Society 1995;4(1):113-25.
1995: N Isakov; R L Wange; W H Burgess; Julian D Watts; Ruedi Aebersold; Lawrence E Samelson
ZAP-70 binding specificity to T cell receptor tyrosine-based activation motifs: the tandem SH2 domains of ZAP-70 bind distinct tyrosine-based activation motifs with varying affinity.
The Journal of experimental medicine 1995;181(1):375-80.
1994: Julian D Watts; M Affolter; D L Krebs; R L Wange; Lawrence E Samelson; Ruedi Aebersold
Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.
The Journal of biological chemistry 1994;269(47):29520-9.
1994: M Affolter; Julian D Watts; D L Krebs; Ruedi Aebersold
Evaluation of two-dimensional phosphopeptide maps by electrospray ionization mass spectrometry of recovered peptides.
Analytical biochemistry 1994;223(1):74-81.
1994: Michael Robert Gold; R Chiu; RJ Ingham; T M Saxton; I van Oostveen; Julian D Watts; M Affolter; Ruedi Aebersold
Activation and serine phosphorylation of the p56lck protein tyrosine kinase in response to antigen receptor cross-linking in B lymphocytes.
Journal of immunology (Baltimore, Md. : 1950) 1994;153(6):2369-80.
1994: T M Saxton; I van Oostveen; D Bowtell; Ruedi Aebersold; Michael Robert Gold
B cell antigen receptor cross-linking induces phosphorylation of the p21ras oncoprotein activators SHC and mSOS1 as well as assembly of complexes containing SHC, GRB-2, mSOS1, and a 145-kDa tyrosine-phosphorylated protein.
Journal of immunology (Baltimore, Md. : 1950) 1994;153(2):623-36.
1994: S Miao; L Ziser; Ruedi Aebersold; Stephen G Withers
Identification of glutamic acid 78 as the active site nucleophile in Bacillus subtilis xylanase using electrospray tandem mass spectrometry.
Biochemistry 1994;33(23):7027-32.
1994: R Winz; daniel Hess; Ruedi Aebersold; Roger Brownsey
Unique structural features and differential phosphorylation of the 280-kDa component (isozyme) of rat liver acetyl-CoA carboxylase.
The Journal of biological chemistry 1994;269(20):14438-45.
1994: S Miao; John McCarter; M E Grace; G A Grabowski; Ruedi Aebersold; Stephen G Withers
Identification of Glu340 as the active-site nucleophile in human glucocerebrosidase by use of electrospray tandem mass spectrometry.
The Journal of biological chemistry 1994;269(15):10975-8.
1994: K W Harder; P Owen; L K Wong; Ruedi Aebersold; Ian Clark-Lewis; Frank R Jirik
Characterization and kinetic analysis of the intracellular domain of human protein tyrosine phosphatase beta (HPTP beta) using synthetic phosphopeptides.
The Biochemical journal 1994;298 ( Pt 2)():395-401.
1994: Michael Robert Gold; T Yungwirth; C L Sutherland; RJ Ingham; D Vianzon; R Chiu; I van Oostveen; H D Morrison; Ruedi Aebersold
Purification and identification of tyrosine-phosphorylated proteins from B lymphocytes stimulated through the antigen receptor.
Electrophoresis 1994;15(3-4):441-53.
1994: Michael Robert Gold; Vincent Duronio; S P Saxena; John W Schrader; Ruedi Aebersold
Multiple cytokines activate phosphatidylinositol 3-kinase in hemopoietic cells. Association of the enzyme with various tyrosine-phosphorylated proteins.
The Journal of biological chemistry 1994;269(7):5403-12.
1994: Michael Robert Gold; Ruedi Aebersold
Both phosphatidylinositol 3-kinase and phosphatidylinositol 4-kinase products are increased by antigen receptor signaling in B cells.
Journal of immunology (Baltimore, Md. : 1950) 1994;152(1):42-50.
1993: Julian D Watts; Melanie J Welham; L Kalt; John W Schrader; Ruedi Aebersold
IL-2 stimulation of T lymphocytes induces sequential activation of mitogen-activated protein kinases and phosphorylation of p56lck at serine-59.
Journal of immunology (Baltimore, Md. : 1950) 1993;151(12):6862-71.
1993: Julian D Watts; Jasbinder S Sanghera; Steven Pelech; Ruedi Aebersold
Phosphorylation of serine 59 of p56lck in activated T cells.
The Journal of biological chemistry 1993;268(31):23275-82.
1993: Nicolai S C van Oers; W Tao; Julian D Watts; Pauline Johnson; Ruedi Aebersold; Hung-Sia Teh
Constitutive tyrosine phosphorylation of the T-cell receptor (TCR) zeta subunit: regulation of TCR-associated protein tyrosine kinase activity by TCR zeta.
Molecular and cellular biology 1993;13(9):5771-80.
1993: daniel Hess; T C Covey; R Winz; Roger Brownsey; Ruedi Aebersold
Analytical and micropreparative peptide mapping by high performance liquid chromatography/electrospray mass spectrometry of proteins purified by gel electrophoresis.
Protein science : a publication of the Protein Society 1993;2(8):1342-51.
1993: Q Wang; D Tull; A Meinke; Neil Gilkes; R Antony J Warren; Ruedi Aebersold; Stephen G Withers
Glu280 is the nucleophile in the active site of Clostridium thermocellum CelC, a family A endo-beta-1,4-glucanase.
The Journal of biological chemistry 1993;268(19):14096-102.
1992: S Kim; P Sandusky; N R Bowlby; Ruedi Aebersold; Beverley R Green; S Vlahakis; Charles F Yocum; Eran Pichersky
Characterization of a spinach psbS cDNA encoding the 22 kDa protein of photosystem II.
FEBS letters 1992;314(1):67-71.
1992: Beverley R Green; D Shen; Ruedi Aebersold; Eran Pichersky
Identification of the polypeptides of the major light-harvesting complex of photosystem II (LHCII) with their genes in tomato.
FEBS letters 1992;305(1):18-22.
1992: J C Gebler; Ruedi Aebersold; Stephen G Withers
Glu-537, not Glu-461, is the nucleophile in the active site of (lac Z) beta-galactosidase from Escherichia coli.
The Journal of biological chemistry 1992;267(16):11126-30.
1992: Ruedi Aebersold; E J Bures; M Namchuk; M H Goghari; B Shushan; T C Covey
Design, synthesis, and characterization of a protein sequencing reagent yielding amino acid derivatives with enhanced detectability by mass spectrometry.
Protein science : a publication of the Protein Society 1992;1(4):494-503.
1992: E Ettehadieh; Jasbinder S Sanghera; Steven Pelech; D Hess-Bienz; J Watts; N Shastri; Ruedi Aebersold
Tyrosyl phosphorylation and activation of MAP kinases by p56lck.
Science (New York, N.Y.) 1992;255(5046):853-5.
1992: Julian D Watts; G M Wilson; E Ettenhadieh; Ian Clark-Lewis; C A Kubanek; Caroline R Astell; Jamey D Marth; Ruedi Aebersold
Purification and initial characterization of the lymphocyte-specific protein-tyrosyl kinase p56lck from a baculovirus expression system.
The Journal of biological chemistry 1992;267(2):901-7.
1991: Neil Gilkes; Marc Claeyssens; Ruedi Aebersold; Bernard Henrissat; A Meinke; H D Morrison; Douglas G Kilburn; R Antony J Warren; R C Miller
Structural and functional relationships in two families of beta-1,4-glycanases.
European journal of biochemistry / FEBS 1991;202(2):367-77.
1991: Ruedi Aebersold; Julian D Watts; H D Morrison; E J Bures
Determination of the site of tyrosine phosphorylation at the low picomole level by automated solid-phase sequence analysis.
Analytical biochemistry 1991;199(1):51-60.
1991: E Schwartz; R Stasys; Ruedi Aebersold; J M McGrath; Beverley R Green; Eran Pichersky
Sequence of a tomato gene encoding a third type of LHCII chlorophyll a/b-binding polypeptide.
Plant molecular biology 1991;17(4):923-5.
1991: D Tull; Stephen G Withers; Neil Gilkes; Douglas G Kilburn; R Antony J Warren; Ruedi Aebersold
Glutamic acid 274 is the nucleophile in the active site of a "retaining" exoglucanase from Cellulomonas fimi.
The Journal of biological chemistry 1991;266(24):15621-5.
1991: J Babcook; J Watts; Ruedi Aebersold; Hermann J Ziltener
Automated nonisotopic assay for protein-tyrosine kinase and protein-tyrosine phosphatase activities.
Analytical biochemistry 1991;196(2):245-51.
1991: Eran Pichersky; R Subramaniam; M J White; J Reid; Ruedi Aebersold; Beverley R Green
Chlorophyll a/b binding (CAB) polypeptides of CP29, the internal chlorophyll a/b complex of PSII: characterization of the tomato gene encoding the 26 kDa (type I) polypeptide, and evidence for a second CP29 polypeptide.
Molecular & general genetics : MGG 1991;227(2):277-84.
1991: Ian Clark-Lewis; Bernhard Moser; A Walz; Marco Baggiolini; G J Scott; Ruedi Aebersold
Chemical synthesis, purification, and characterization of two inflammatory proteins, neutrophil activating peptide 1 (interleukin-8) and neutrophil activating peptide.
Biochemistry 1991;30(12):3128-35.
1991: E Schwartz; D Shen; Ruedi Aebersold; J M McGrath; Eran Pichersky; Beverley R Green
Nucleotide sequence and chromosomal location of Cab11 and Cab12, the genes for the fourth polypeptide of the photosystem I light-harvesting antenna (LHCI).
FEBS letters 1991;280(2):229-34.
1990: Jasbinder S Sanghera; Ruedi Aebersold; H D Morrison; E J Bures; Steven Pelech
Identification of the sites in myelin basic protein that are phosphorylated by meiosis-activated protein kinase p44mpk.
FEBS letters 1990;273(1-2):223-6.
1990: Ruedi Aebersold; H D Morrison
Analysis of dilute peptide samples by capillary zone electrophoresis.
Journal of chromatography 1990;516(1):79-88.
1990: G B Kalmar; R J Kay; A Lachance; Ruedi Aebersold; Rosemary B Cornell
Cloning and expression of rat liver CTP: phosphocholine cytidylyltransferase: an amphipathic protein that controls phosphatidylcholine synthesis.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(16):6029-33.
1990: Ruedi Aebersold; J Leavitt
Sequence analysis of proteins separated by polyacrylamide gel electrophoresis: towards an integrated protein database.
Electrophoresis 1990;11(7):517-27.