Phenyx Publications (Updated April 2010)
2010:
xComb: A cross-link peptide database approach to protein-protein interaction analysis.
J. Proteome Res., Publication Date (Web): 19 March 2010
Alexandre Panchaud1,2, Pragya Singh1, Scott A. Shaffer1, and David Goodlett1
1 Department of Medicinal Chemistry, University of Washington, Seattle, WA; 2 Current address: Nestle Research Center, Lausanne, Switzerland
DOI: 10.1021/pr9011816
Early activation of the fatty acid metabolism pathway by chronic high glucose exposure in rat insulin secretory β-cells
Proteomics 2010 Volume 10 Issue 1
Yohann Couté, Yannick Brunner, Domitille Schvartz, Céline Hernandez, Alexandre Masselot, Frédérique Lisacek, Claes B. Wollheim, Jean-Charles Sanchez
Biomedical Proteomics Research Group, Structural Biology and Bioinformatics Department, Centre Médical Universitaire, Geneva, Switzerland. Proteome Informatics Group, Swiss Institute of Bioinformatics, Centre Médical Universitaire, Geneva, Switzerland. Geneva Bioinformatics (GeneBio) SA, Geneva, Switzerland. Department of Cell Physiology and Metabolism, University Medical Center, Geneva, Switzerland
Isobaric tagging-based selection and quantitation of CSF tryptic peptides with reporter calibration curves
Analytical chemistry Publication Date (Web): January 8, 2010
Loïc Dayon, Natacha Turck, Stefan Kienle, Peter Schulz-Knappe, Denis F. Hochstrasser, Alexander Scherl and Jean-Charles Sanchez
Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
DOI: 10.1021/ac901854k
2009:
Systems biology meets synthetic biology: a case study of the metabolic effects of synthetic rewiring
Mol. BioSyst., 2009, 5, 1214 - 1223
Josselin Noirel, Saw Yen Ow, Guido Sanguinetti and Phillip C. Wright
ChELSI Research Institute, The Sheffield Bioincubator, Department of Chemical and Process Engineering, University of Sheffield, Mappin St, Sheffield, United Kingdom S1 3JD; Department of Computer Science, University of Sheffield, 211 Portobello St, Sheffield, United Kingdom S1 4DP
DOI: 10.1039/b904729h
Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach
Molecular & Cellular Proteomics, 2009 - Revised on August 26, 2009 Accepted on September 15, 2009
Stuart A. Cain, Amanda McGovern, Elaine Small, Lyle J. Ward, Clair Baldock, Adrian Shuttleworth and Cay M. Kielty
Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, United Kingdom
DOI: 10.1074/mcp.M900008-MCP200
Quantitative Proteomic Analysis of Sulfolobus solfataricus Membrane Proteins
J. Proteome Res., Publication Date (Web): December 2, 2009
Trong Khoa Pham, Pawel Sierocinski, John Van Der Oost and Phillip Craig Wright
ChELSI Institute, Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield; Laboratory of Microbiology, Wageningen University, The Netherlands
DOI: 10.1021/pr9007688
Mass spectrometric characterization of mitochondrial complex I NDUFA10 variants
Proteomics 2008, 8, 1898-1908
Javier Muñoz, Joaquín Fernández-Irigoyen, Enrique Santamaría, Axel Parbel, José Obeso, Dr. Fernando J. Corrales
Division of Hepatology and Gene Therapy, Proteomics Unit and Division of Neurosciences, Center for Applied Medical Research (CIMA), University Hospital of Navarra (CUN), University of Navarra, Pamplona, Spain, GE Healthcare, Munich, Germany
DOI: 10.1002/pmic.200701085
Identification of Replication-competent HSV-1 Cgal Strain Signaling Targets in Human Hepatoma Cells by Functional Organelle Proteomics
Molecular & Cellular Proteomics 8:805-815, 2009
Enrique Santamaría, María I. Mora, Corinne Potel, Joaquín Fernández-Irigoyen, Elvira Carro-Roldán, Rubén Hernández-Alcoceba, Jesús Prieto, Alberto L. Epstein and Fernando J. Corrales
From the Division of Hepatology and Gene Therapy, Proteomics Unit, Centre for Applied Medical Research, University of Navarra, 31008 Pamplona, Spain and Université Lyon 1, Lyon F-69003, France, CNRS, UMR5534, Centre de Génétique Moleculaire et Cellulaire, 16 rue Dubois, Villeurbanne, F-69622, France
DOI: 10.1074/mcp.M800202-MCP200
SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid
PROTEOMICS Volume 9, Issue 10, Date: No. 10 May 2009
Andreas Quandt, Alexandre Masselot, Patricia Hernandez, Céline Hernandez, Sergio Maffioletti, Ron D. Appel, Frederique Lisacek
Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland, Geneva Bioinformatics (GeneBio) S.A., Geneva, Switzerland, Swiss National Supercomputing Centre, Manno, Switzerland, University of Geneva, Computer Science Department, Geneva, Switzerland
Published Online: 24 Apr 2009; DOI: 10.1002/pmic.200800207
A simple workflow to increase MS2 identification rate by subsequent spectral library search
Proteomics 9(6):1731-6, 2009 Mar
Erik Ahrné, Alexandre Masselot, Pierre-Alain Binz, Markus Müller, Frederique Lisacek
Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland, Geneva Bioinformatics (Genebio) SA, Geneva, Switzerland
DOI: 10.1002/pmic.200800410
Effects of cigarette smoking on the human urinary proteome
Biochemical and Biophysical Research Communications Volume 381, Issue 3, 10 April 2009, Pages 397-402, Available online 15 February 2009
Luisa Airoldi, Cinzia Magagnotti, Angela Rita Iannuzzi, Cristina Marelli, Renzo Bagnati, Roberta Pastorelli, Alessandro Colombi, Stefano Santaguida, Chiara Chiabrando, Silvia Schiarea and Roberto Fanelli
Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, via Giuseppe La Masa, 19, 20156 Milan, Italy
DOI: 10.1016/j.bbrc.2009.02.055
Dioxin-Sensitive Proteins in Differentiating Osteoblasts: Effects on Bone Formation In Vitro
Toxicological Sciences 2009 108(2):330-343; accepted January 27, 2009
Donatella Carpi, Merja Korkalainen, Luisa Airoldi, Roberto Fanelli, Helen Hakansson, Virpi Muhonen, Juha Tuukkanen, Matti Viluksela and Roberta Pastorelli
Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy, Department of Environmental Health, National Public Health Institute, Kuopio, Finland, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden, Institute of Biomedicine, Department of Anatomy and Cell Biology, University of Oulu, Oulu, Finland
DOI: 10.1093/toxsci/kfp021
Comparison of electrospray and matrix-assisted laser desorption ionization on the same hybrid quadrupole time-of-flight tandem mass spectrometer application to bidimensional liquid chromatography of proteins from bovine milk fraction
Journal of Chromatography. Accepted 12 January 2009. Available online 15 January 2009
Daniel Mollé1,2, Julien Jardin1,2, Michel Piot1,2, Maryvonne Pasco1,2, Joëlle Léonil1,2, Valérie Gagnaire1,2
1 INRA, UMR1253, F-35000 Rennes, France
2 Agrocampus-Ouest, UMR1253, F-35000 Rennes, France
DOI: 10.1016/j.chroma.2009.01.017
Temporal Quantitative Proteomics by iTRAQ 2D-LC-MS/MS and Corresponding mRNA Expression Analysis Identify Post-Transcriptional Modulation of Actin-Cytoskeleton Regulators During TGF-β-Induced Epithelial-Mesenchymal Transition
J. Proteome Res., 2009, 8 (1), pp 35-47 Publication Date (Web): January 2, 2009
Venkateshwar G. Keshamouni, Pratik Jagtop, George Michailidis, John R. Stahler, Rork Kuick, Ajaya Kumar Reka, Panagiotis Papoulias, Rashmi Krishmapuram, Anjaiah Srirangam, Theodore J. Standiford, Philip C. Andrews and Gilbert S. Omenn
Divisions of Pulmonary and Critical Care Medicine and of Molecular Medicial Genetics, Department of Internal Medicine, Michigan Proteome Consortium, National Resource for Proteomics and Pathways, and Department of Biological Chemistry, Department of Statistics, Biostatistics Core, Comprehensive Cancer Center, Department of Human Genetics, and Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, 48109, and, Department of Medicine, Indiana University, Indianapolis, Indiana 46202
DOI: 10.1021/pr8006478
2008:
Proteomic Analysis of Human Bile from Malignant Biliary Stenosis Induced by Pancreatic Cancer
J. Proteome Res., 2009, 8 (1), pp 159-169 Publication Date (Web): December 5, 2008
Annarita Farina, Jean-Marc Dumonceau, Jean-Louis Frossard, Antoine Hadengue, Denis F. Hochstrasser and Pierre Lescuyer
Biomedical Proteomics Research Group, Department of Bioinformatics and Structural Biology, Faculty of Medicine, Geneva University, Geneva CH-1211, Switzerland, Service of Gastroenterology and Hepatology, Geneva University Hospitals, Geneva CH-1211, Switzerland, and Laboratory Medicine Service, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva CH-1211, Switzerland
DOI: 10.1021/pr8004925
Characterization of Protein Cross-Links via Mass Spectrometry and an Open-Modification Search Strategy
Anal. Chem., 2008, 80 (22), pp 8799-8806 Publication Date (Web): October 24, 2008
Pragya Singh, Scott A. Shaffer, Alexander Scherl, Carol Holman, Richard A. Pfuetzner, Theodore J. Larson Freeman, Samuel I. Miller, Patricia Hernandez, Ron D. Appel and David R. Goodlett
Departments of Medicinal Chemistry, Molecular and Cellular Biology, Genome Sciences, and Medicine, University of Washington, Seattle, Washington 98195, Swiss Institute of Bioinformatics, Geneva, Switzerland, and Department of Computer Science, University of Geneva, Geneva, Switzerland
DOI: 10.1021/ac801646f
pICarver: A Software Tool and Strategy for Peptides Isoelectric Focusing
J. Proteome Res., 2008, 7 (10), pp 4336-4345 Publication Date (Web): September 11, 2008
Ali R. Vaezzadeh, Céline Hernandez, Oscar Vadas, Jacques J. M. Deshusses, Pierre Lescuyer, Frédérique Lisacek and Denis F. Hochstrasser
Biomedical Proteomics Research Group, Department of Bioinformatics and Structural Biology, Geneva University, 1 Michel Servet, 1211 Geneva, Switzerland, Swiss Institute of Bioinformatics, Geneva University, 1 Michel Servet, 1211 Geneva, Switzerland, Department of Structural Biology and Bioinformatics, Geneva University, 1 Michel Servet, 1211 Geneva, Switzerland, and Clinical Proteomics Laboratory, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
DOI: 10.1021/pr8002672
On the benefits of acquiring peptide fragment ions at high measured mass accuracy.
J Am Soc Mass Spectrom. Volume 19, Issue 6, June 2008, Pages 891-901.
Scherl A, Shaffer SA, Taylor GK, Hernandez P, Appel RD, Binz PA, Goodlett DR.
Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA; Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland; Geneva Bioinformatics SA, Geneva, Switzerland
DOI: 10.1016/j.jasms.2008.02.005
Apolipoprotein(a) Size and Lipoprotein(a) Concentrations in Patients with Good and Poor Coronary Collateral Flow - an Interrelation Discovered by Proteomic Screening of Pooled Plasma Sam
Journal of Proteomics and Bioinformatics; Received August 20, 2008; Accepted October 17, 2008; Published November 05, 2008
Daniel Stalder, Trinh Cung, Steffen Gloekler1, Pascal Meier1, Evelyn Schlappritzi, André Haeberli, Santica Marcovina2, Christian Seiler1, Manfred Heller
Laboratory of Thrombosis Research, Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
1 Department of Cardiology, University Hospital, Bern, Switzerland
2 Northwest Lipid Metabolism and Diabetes Research Laboratory, University of Washington, Seattle, WA, USA
Proteomic Comparison between Two Marine Snail Ecotypes Reveals Details about the Biochemistry of Adaptation
J. Proteome Res., 2008, 7 (11), pp 4926-4934. Publication Date (Web): October 20, 2008
Monica Martinez-Fernandez, Ana M. Rodriguez-Pineiro, Eliandre Oliveira, Maria Paez de la Cadena and Emilio Rolan-Alvarez
Departamento de Bioquimica, Genetica e Inmunologia. Facultad de Biologia, Universidad de Vigo, Campus Universitario, 36310 Vigo, Spain, and Plataforma de Proteomica, Parc Cientific de Barcelona, Universitat de Barcelona, C/ Josep Samitier, 1-5, 08028 Barcelona, Spain
DOI: 10.1021/pr700863e
Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies
Proteome Res., 2008, 7 (1), pp 245-253. Publication Date (Web): January 4, 2008
Brian C. Searle, Mark Turner, and Alexey I. Nesvizhskii
Proteome Software Inc., 1340 S.W. Bertha Boulevard, Suite 201, Portland, Oregon 97219-2039, and Department of Pathology and Center for Computational Medicine and Biology, University of Michigan, 1301 Catherine Road, Ann Arbor, Michigan 48109-0602
DOI: 10.1021/pr070540w
Identification of replication-competent HSV-1 Cgal+ strain signalling targets in human hepatoma cells by functional organelle proteomics
Mol. Cell. Proteomics, Dec 2008.
Enrique Santamaría, María I. Mora, Corinne Potel, Joaquín Fernández-Irigoyen, Elvira Carro-Roldán, Rubén Hernández-Alcoceba, Jesús Prieto, Alberto L. Epstein, and Fernando J. Corrales
Proteomics laboratory, Applied Medical Research Center (CIMA), Pamplona, Navarra 31008
DOI: 10.1074/mcp.M800202-MCP200
Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses
Proteomics 2008, 8, 2791-2797. Received: January 15, 2008 Revised: March 7, 2008 Accepted: March 30, 2008.
Alexander Scherl, Yihsuan Shannon Tsai, Scott A. Shaffer and David R. Goodlett
Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
DOI: 10.1002/pmic.200800045
Mapping of macrophage elastase cleavage sites in insoluble human skin elastin
Matrix Biology 27 (2008) 420-428. (Elsevier) Received 24 December 2007; Received in revised form 3 February 2008; Accepted 4 February 2008.
Samuel Taddese1, Anthony S. Weiss2, Reinhard H.H. Neubert1, Christian E.H. Schmelzer1,2
1 Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
2 School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia
Membrane protein identifications by mass spectrometry using electrocapture-based separation as part of a two-dimensional fractionation system
Analytical Biochemistry Volume 381, Issue 1, 1 October 2008, Pages 33-42. Received 18 March 2008. Available online 27 June 2008.
Juan Astorga-Wells, Sam Tryggvason, Susanne Vollmer, Gunvor Alvelius, Carina Palmberg and Hans Jörnvall
Department of Medical Biochemistry and Biophysics, Karolinska Instituttet, SE-171 77 Stockholm, Sweden
Proteomic analysis of the porcine platelet proteome and alterations induced by thrombin activation
Journal of Proteomics Volume 71, Issue 5, 2 December 2008, Pages 547-560. Received 1 July 2008; Accepted 28 August 2008; Available online 7 September 2008.
Gloria Esteso1, María Isabel Mora2, Juan José Garrido1, Fernando Corrales2, Ángela Moreno1
1 Unidad Mixta C.S.I.C.-UCO "Marcadores Genéticos Moleculares en Animales Domésticos", Departamento de Genética, Universidad de Córdoba, Campus Rabanales, Edificio Gregor Mendel (C-5), 14071 Córdoba, Spain
2 Unidad de Proteómica, Centro de Investigaciones Médicas Aplicadas, Universidad de Navarra, Edificio CIMA, Pio XII 55, Pamplona, Spain
In vitro degradation of human tropoelastin by MMP-12 and the generation of matrikines from domain 24
Matrix Biology. Received 5 October 2008; Received in revised form 16 November 2008; Accepted 10 December 2008.
Samuel Taddese1, Anthony S.Weiss2, Günther Jahreis3, Reinhard H.H. Neubert1, Christian E.H. Schmelzer1
1 Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
2 School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia
3 Max Planck Research Unit for Enzymology of Protein Folding, Halle (Saale), Germany
DOI: 10.1016/j.matbio.2008.12.002
Comparison of electrospray and matrix-assisted laser desorption ionization on the same hybrid quadrupole time-of-flight tandem mass spectrometer application to bidimensional liquid chromatography of proteins from bovine milk fraction
Journal of Chromatography. Received 11 July 2008; Revised 5 January 2009; Accepted 12 January 2009. Available online 15 January 2009.
Daniel Mollé1,2, Julien Jardin1,2, Michel Piot1,2, Maryvonne Pasco1,2, Joëlle Léonil1,2, Valérie Gagnaire1,2
1 INRA, UMR1253, F-35000 Rennes, France
2 Agrocampus-Ouest, UMR1253, F-35000 Rennes, France
DOI: 10.1016/j.chroma.2009.01.017
Identification of N-linked glycoproteins in human milk by hydrophilic interaction liquid chromatography and mass spectrometry
Proteomics 2008, 8, 3833-3847. Received November 13, 2007; Revised April 24, 2008; Accepted May 15, 2008.
Gianluca Picariello1, Pasquale Ferranti2, Gianfranco Mamone1, Peter Roepstorff3 and Francesco Addeo1,2
1 Istituto di Scienze dell'Alimentazione - CNR, Avellino, Italy
2 Dipartimento di Scienza degli Alimenti, University of Naples "Federico II", Portici (NA), Italy
3 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
DOI: 10.1002/pmic.200701057
Proteomic profiling in an animal model of acute pancreatitis
Proteomics 2008, 8, 3621-3631. Received January 23, 2008; Revised April 14, 2008; Accepted May 6, 2008.
Vanessa Fétaud1, Jean-Louis Frossard2, Annarita Farina1, Catherine M. Pastor2, Léo Bühler3, Jean-Marc Dumonceau2, Antoine Hadengue2, Denis F. Hochstrasser1,4 and Pierre Lescuyer1,4
1 Biomedical Proteomics Research Group, Department of Bioinformatics and Structural Biology, Geneva Faculty of Medicine, Geneva, Switzerland
2 Division of Gastroenterology and Hepatology, Geneva University Hospitals, Geneva, Switzerland
3 Surgical Research Unit, Department of Surgery, Geneva University Hospitals, Geneva, Switzerland
4 Clinical Proteomics Laboratory, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
DOI: 10.1002/pmic.200800066
Imaging mass spectrometry using peptide isoelectric focusing
Rapid Commumications in Mass Spectrometry 2008; 22: 2667-2676. Received 25 April 2008; Revised 20 June 2008; Accepted 25 June 2008; Available online 1 August 2008.
Ali R. Vaezzadeh1, Jovan Simicevic1, Alexis Chauvet1, Patrice François2, Catherine G. Zimmermann-Ivol1, Pierre Lescuyer1, Jacques P. M. Deshusses1 and Denis F. Hochstrasser1
1 Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Geneva University, 1 rue Michel Servet, 1211 Geneva, Switzerland
2 Genomic Research Laboratory, Geneva University Hospital, Geneva, Switzerland
DOI: 10.1002/rcm.3658
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program
Journal of Proteomics. Available online 24 November 2008.
Michel Schneider1, Lydie Lane1, Emmanuel Boutet1, Damien Lieberherr1, Michael Tognolli1, Lydie Bougueleret1, Amos Bairoch1,2
1 Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel Servet, 1211 Genève 4, Switzerland
2 Department of Structural Biology and Bioinformatics, Centre Médical Universitaire, 1 rue Michel Servet, 1211 Genève 4, Switzerland
DOI: 10.1016/j.jprot.2008.11.010
Proteomic analysis of a podocyte vesicle-enriched fraction from human normal and pathological urine samples
PROTEOMICS Clinical Applications Volume 2 Issue 7-8, Pages 1008-1018. Special Issue: Renal and Urinary Proteomics. Published Online 10 July 2008.
Pierre Lescuyer1, Agnès Pernin2, Alexandre Hainard1, Caty Bigeire2, Jennifer A. Burgess1, Catherine Zimmermann-Ivol1, Jean-Charles Sanchez1, Jürg A. Schifferli3, Denis F. Hochstrasser1, Solange Moll, Dr.2
1 Biomedical Proteomics Research Group, University Hospital, Geneva, Switzerland
2 Institute of Clinical Pathology, Department of Genetic and Laboratory Medicine, University Hospital, Geneva, Switzerland
3 Laboratory of Immunonephrology, University Hospital, Basel, Switzerland
DOI: 10.1002/prca.200800033
On the benefits of acquiring peptide fragment ions at high measured mass accuracy.
J Am Soc Mass Spectrom. 2008 Jun;19(6):891-901. Epub 2008 Mar 4.
Scherl A, Shaffer SA, Taylor GK, Hernandez P, Appel RD, Binz PA, Goodlett DR.
Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
Evaluation of reproducibility of protein identification results after multidimensional human serum protein separation
Proteomics 2008, 8, 414-424. Received June 4, 2007; Revised October 11, 2007; Accepted November 1, 2007.
Daniel Stalder, André Haeberli and Manfred Heller
Laboratory of Thrombosis Research, Department of Clinical Research, University of Berne, Berne, Switzerland
DOI: 10.1002/pmic.200700527
Proteomic analysis of wheat proteins recognized by IgE antibodies of allergic patients
Proteomics 2008, 8, 1677-1691. Received April 10, 2007; Revised November 28, 2007; Accepted December 11, 2007.
Petr Sotkovský1, Martin Hubálek2, Lenka Hernychová2, Petr Novák3, Marie Havranová4, Iva Setinová4, Andrea Kitanovičová1, Martin Fuchs5, Jiří Stulík2 and Ludmila Tučková1
1 Department of Immunology and Gnotobiology, Institute of Microbiology v.v.i, Czech Academy of Sciences, Prague, Czech Republic
2 Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Hradec Kralové, Czech Republic
3 Department of Biogenesis and Biotechnology of Natural Compounds, Institute of Microbiology v.v.i, Czech Academy of Sciences, Prague, Czech Republic
4 Imumed, Prague, Czech Republic
5 Department of Pediatrics, Hospital Bulovka, Prague, Czech Republic
DOI: 10.1002/pmic.200700347
Experimental and computational approaches to quantitative proteomics: Status quo and outlook
Journal of Proteomics Volume 71, Issue 1, 30 April 2008, Pages 19-33. Received 1 October 2007; Accepted 18 December 2007; Available online 23 December 2007.
Alexandre Panchaud1,2, Michael Affolter2, Philippe Moreillon2, and Martin Kussmann2
1 Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
2 Functional Genomics Group, Department of Bioanalytical Science, Nestlé Research Centre, Vers-chez-les-Blanc, P.O. Box 44, CH-1000 Lausanne 26, Switzerland
DOI: 10.1016/j.jprot.2007.12.001
Mapping of macrophage elastase cleavage sites in insoluble human skin elastin
Matrix Biology 27 (2008) 420 - 428 (Elsevier)
Samuel Taddesea, Anthony S. Weissb, Reinhard H.H. Neuberta, Christian E.H. Schmelzera,b
a Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
b School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia
Received 24 December 2007; received in revised form 3 February 2008; accepted 4 February 2008
2007:
Peptide Fragment Intensity Statistical Modeling
Anal. Chem., 2007, 79 (19), pp 7286-7290. Publication Date (Web): August 23, 2007
Jacques Colinge
Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 19/3, A-1090 Vienna, Austria
DOI: 10.1021/ac070488n
Nitric Oxide and Oxygen Radical Attack on GDP-Dissociation Inhibitor 2 (GDI-2) in Spinal Cord Injury of the Rat
J. Proteome Res.; (Article); 2007; 6(4); 1500-1509.
John, J. P. P.; Pintsov, O.; Petter-Puchner, A.; Redl, H.; Pollak, A.; Chen, W.-Q.; Lubec, G.
Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Vienna, Austria
DOI: 10.1021/pr060620k
Assessing peptide de novo sequencing algorithms performance on large and diverse data sets
Proteomics 2007, 7, 3051-3054. Received March 5, 2007; Revised May 9, 2007; Accepted May 30, 2007.
Erik Pitzer1, Alexandre Masselot2 and Jacques Colinge1
1 Bioinformatics Department, Upper Austria University of Applied Sciences at Hagenberg, Hagenberg, Austria
2 Geneva Bioinformatics SA, Genève, Switzerland
DOI: 10.1002/pmic.200700224
Comparative Urine Analysis by Liquid Chromatography-Mass Spectrometry and Multivariate Statistics: Method Development, Evaluation, and Application to Proteinuria
J. Proteome Res.; (Article); 2007; 6(1); 194-206.
Kemperman, R. F. J.; Horvatovich, P. L.; Hoekman, B.; Reijmers, T. H.; Muskiet, F. A. J.; Bischoff, R.
Department of Analytical Biochemistry, University Centre for Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
DOI: 10.1021/pr060362r
Mass Spectrometric Studies on Mouse Hippocampal Synapsins Ia, IIa, and IIb and Identification of a Novel Phosphorylation Site at Serine-546
J. Proteome Res.; (Article); 2007; 6(7); 2695-2710.
John, J. P. P.; Chen, W.-Q.; Pollak, A.; Lubec, G.
Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria
DOI: 10.1021/pr070157r
Limitations and Pitfalls in Protein Identification by Mass Spectrometry
Chem. Rev.; (Review); 2007; 107(8); 3568-3584.
Lubec, G.; Afjehi-Sadat, L.
Medical University of Vienna, Department of Pediatrics, Waehringer Guertel 18, A-1090 Vienna, Austria
DOI: 10.1021/cr068213f
Compositional Protein Analysis of High Density Lipoproteins in Hypercholesterolemia by Shotgun LC-MS/MS and Probabilistic Peptide Scoring
Mol. Cell. Proteomics, Jun 2007; 6: 1059 - 1072.
Manfred Heller, Evelyn Schlappritzi, Daniel Stalder, Jean-Marc Nuoffer, and André Haeberli
From the Laboratory of Thrombosis Research, Department of Clinical Research, University of Bern and Institute of Clinical Chemistry, University Hospital and University Children's Hospital, 3010 Bern, Switzerland
ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in Ribosome biogenesis
Mol. Cell. Proteomics, Dec 2007.
Yohann Couté, Karine Kindbeiter, Stéphane Belin, Régis Dieckmann, Laurent Duret, Laurent Bezin, Jean-Charles Sanchez, and Jean-Jacques Diaz
Biomedical Proteomics Research Group, Département de Biologie Structurale et Bioinformatique, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
DOI: 10.1074/mcp.M700510-MCP200
Proteomics Analysis of Insulin Secretory Granules
Mol. Cell. Proteomics, Jun 2007; 6: 1007-1017.
Yannick Brunner, Yohann Couté, Mariella Iezzi, Michelangelo Foti, Mitsonuri Fukuda, Denis F. Hochstrasser, Claes B. Wollheim, and Jean-Charles Sanchez
Biomedical Proteomics Research Group, University Medical Center, 1211 Geneva 4, Switzerland
Identification of specific reachable molecular targets in human breast cancer using a versatile ex vivo proteomic method
Proteomics 2007, 7, 1188-1196.
Vincent Castronovo1, Philippe Kischel1, Francois Guillonneau2, Laurence de Leval3, Thierry Deféchereux4, Edwin De Pauw2, Dario Neri5 and David Waltregny1
1 Metastasis Research Laboratory, Center for Experimental Cancer Research, University of Liège, Liège, Belgium
2 Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, Liège, Belgium
3 Department of Pathology, University Hospital of Liège, Liège, Belgium
4 Department of Abdominal Surgery and Transplantation, University Hospital of Liège, Liège, Belgium
5 Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland
DOI: 10.1002/pmic.200600888
Proteomics Demonstration That Normal Breast Epithelial Cells Can Induce Apoptosis of Breast Cancer Cells through Insulin-like Growth Factor-binding Protein-3 and Maspin
Mol. Cell. Proteomics, Jul 2007; 6: 1239 - 1247.
Robert-Alain Toillon, Chann Lagadec, Adeline Page, Valérie Chopin, Pierre-Eric Sautière, Jean-Marc Ricort, Jérôme Lemoine, Ming Zhang, Hubert Hondermarck, and Xuefen Le Bourhis
INSERM ERI-8 (JE 2488) Signalisation des facteurs de croissance dans le cancer du sein. Protéomique fonctionnelle, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq, France
Nerve Growth Factor Receptor TrkA Signaling in Breast Cancer Cells Involves Ku70 to Prevent Apoptosis
Mol. Cell. Proteomics, Nov 2007; 6: 1842 - 1854.
Emmanuelle Com, Chann Lagadec, Adeline Page, Ikram El Yazidi-Belkoura, Christian Slomianny, Ambre Spencer, Djilali Hammache, Brian B. Rudkin, and Hubert Hondermarck
INSERM ERI-8 (JE-2488), Growth factor signaling in breast cancer. Functional proteomics, University of Sciences and Technologies Lille, 59655 Villeneuve d'Ascq, France
Phosphorylation of B14.5a Subunit from Bovine Heart Complex I Identified by Titanium Dioxide Selective Enrichment and Shotgun Proteomics
Mol. Cell. Proteomics, Feb 2007; 6: 231 - 237.
Gabriella Pocsfalvi, Manuela Cuccurullo, Gitta Schlosser, Salvatore Scacco, Sergio Papa, and Antonio Malorni
Proteomic and Biomolecular Mass Spectrometry Centre, Institute of Food Science and Technology, Consiglio Nazionale delle Ricerche, 83100 Avellino, Italy
Labeling of Bifidobacterium longum Cells with 13C-Substituted Leucine for Quantitative Proteomic Analyses
Appl Environ Microbiol. 2007 September; 73(17): 5653-5656. Published online 2007 June 29.
Yohann Couté, Céline Hernandez, Ron D. Appel, Jean-Charles Sanchez, and Abelardo Margolles
Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 14, Switzerland
Introduction to Computational Proteomics
PLoS Comput Biol. 2007 July; 3(7): e114. Published online 2007 July 27.
Jacques Colinge and Keiryn L. Bennett
Ce-M-M-, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
Proteome characterization of a human urothelial cell line resistant to the bladder carcinogen 4-aminobiphenyl
Proteome Sci. 2007; 5: 6. Published online 2007 May 3.
Roberta Pastorelli, Federica Saletta, Donatella Carpi, Roberta Campagna, Carlo dell'Osta, Silvia Schiarea, Paolo Vineis, Luisa Airoldi, and Giuseppe Matullo
Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
DOI: 10.1186/1477-5956-5-6
Nitric Oxide and Oxygen Radical Attack on GDP-Dissociation Inhibitor 2 (GDI-2) in Spinal Cord Injury of the Rat
J. Proteome Res.; (Article); 2007; 6(4); 1500-1509.
John, J. P. P.; Pintsov, O.; Petter-Puchner, A.; Redl, H.; Pollak, A.; Chen, W.-Q.; Lubec, G.
Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Vienna, Austria
DOI: 10.1021/pr060620k
Comparative Urine Analysis by Liquid Chromatography-Mass Spectrometry and Multivariate Statistics: Method Development, Evaluation, and Application to Proteinuria
J. Proteome Res.; (Article); 2007; 6(1); 194-206.
Kemperman, R. F. J.; Horvatovich, P. L.; Hoekman, B.; Reijmers, T. H.; Muskiet, F. A. J.; Bischoff, R.
Department of Analytical Biochemistry, University Centre for Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
DOI: 10.1021/pr060362r
Mass Spectrometric Studies on Mouse Hippocampal Synapsins Ia, IIa, and IIb and Identification of a Novel Phosphorylation Site at Serine-546
J. Proteome Res.; (Article); 2007; 6(7); 2695-2710.
John, J. P. P.; Chen, W.-Q.; Pollak, A.; Lubec, G.
Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria.
DOI: 10.1021/pr070157r
Limitations and Pitfalls in Protein Identification by Mass Spectrometry
Chem. Rev.; (Review); 2007; 107(8); 3568-3584.
Lubec, G.; Afjehi-Sadat, L.
Medical University of Vienna, Department of Pediatrics, Waehringer Guertel 18, A-1090 Vienna, Austria
DOI: 10.1021/cr068213f
Compositional Protein Analysis of High Density Lipoproteins in Hypercholesterolemia by Shotgun LC-MS/MS and Probabilistic Peptide Scoring
Mol. Cell. Proteomics, Jun 2007; 6: 1059 - 1072.
Manfred Heller, Evelyn Schlappritzi, Daniel Stalder, Jean-Marc Nuoffer, and André Haeberli
From the Laboratory of Thrombosis Research, Department of Clinical Research, University of Bern, and The Institute of Clinical Chemistry, University Hospital and University Children's Hospital, 3010 Bern, Switzerland
ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in Ribosome biogenesis
Mol. Cell. Proteomics, Dec 2007.
Yohann Couté, Karine Kindbeiter, Stéphane Belin, Régis Dieckmann, Laurent Duret, Laurent Bezin, Jean-Charles Sanchez, and Jean-Jacques Diaz
Biomedical Proteomics Research Group, Département de Biologie Structurale et Bioinformatique, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland.
DOI: 10.1074/mcp.M700510-MCP200
The minimum information about a proteomics experiment (MIAPE)
Nature Biotechnology 25, 887 - 893 (2007)
Published online: 8 August 2007.
Chris F Taylor1,2, Norman W Paton1,3, Kathryn S Lilley1,4, Pierre-Alain Binz1,5,6, Randall K Julian, Jr1,7, Andrew R Jones1,3, Weimin Zhu1,2, Rolf Apweiler1,2, Ruedi Aebersold1,8, Eric W Deutsch1,9, Michael J Dunn10, Albert J R Heck11, Alexander Leitner12, Marcus Macht13, Matthias Mann14, Lennart Martens1,2, Thomas A Neubert15, Scott D Patterson16, Peipei Ping17, Sean L Seymour1,18, Puneet Souda19, Akira Tsugita20, Joel Vandekerckhove21, Thomas M Vondriska22, Julian P Whitelegge19, Marc R Wilkins23, Ioannnis Xenarios24, John R Yates, III25 & Henning Hermjakob1,2
1 The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
2 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
3 School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
4 Cambridge Centre for Proteomics, University of Cambridge, Cambridge, Cambridgeshire CB2 1QW, UK.
5 Swiss Institute of Bioinformatics, Geneva, Switzerland.
6 Geneva Bioinformatics SA, Geneva, Switzerland.
7 Indigo BioSystems, Indianapolis, Indiana, USA.
8 Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland.
9 Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.
10 Proteome Research Centre, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
11 Utrecht University and Netherlands Proteomics Centre, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
12 Department of Analytical Chemistry and Food Chemistry, University of Vienna, 1090 Vienna, Austria.
13 Bruker Daltonik GmbH, Bremen, Germany.
14 Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany.
15 Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
16 Molecular Sciences, Amgen Inc., Thousand Oaks, California, USA.
17 Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California 90075, USA.
18 Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
19 The Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, and The Molecular Biology Institute, and The Brain Research Institute, University of California, Los Angeles, California 90095, USA.
20 Proteomics Research Laboratory, Tokyo Rikakikai Co., Tsukuba, Japan.
21 Department of Biochemistry, Ghent University and Department of Medical Protein Research, Flanders Institute for Biotechnology, B-9000 Ghent, Belgium.
22 Department of Medicine (Cardiology) and Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.
23 School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia.
24 Serono Pharmaceutical Research Institute, 14, Chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland.
25 The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, California 92037, USA.
DOI: 10.1038/nbt1329
C-Npys (S-3-nitro-2-pyridinesulfenyl) and peptide derivatives can inhibit a serine-thiol proteinase activity from Paracoccidioides brasiliensis
Biochemical and Biophysical Research Communications 355 (2007) 1000 - 1005 (Elsevier)
Alisson L. Matsuo a, Adriana K. Carmona b, Luiz S. Silvaa, Carlos E.L. Cunhab, Ernesto S. Nakayasuc, Igor C. Almeidac, Maria A. Julianob, Rosana Pucciaa
a Department of Microbiology, Immunology and Parasitology, Cell Biology Division, Federal University of Sao Paulo, Sao Paulo, SP 04023-062, Brazil
b Department of Biophysics, Federal University of Sao Paulo, Sao Paulo, SP 04044-062, Brazil
c Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
Received 30 January 2007
Available online 23 February 2007
Characterization of hepatic glutathione S-transferasesin coho salmon (Oncorhynchus kisutch)
Aquatic Toxicology 81 (2007) 126 - 136
Mary Trutea, Byron Gallisb, Catalin Doneanub, Scott Shafferb, David Goodlettb, Evan Gallaghera
a Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105-6099, United States
b Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, United States
Identification of specific reachable molecular targets in human breast cancer using a versatile ex vivo proteomic method
Proteomics 2007, 7, 1188 - 1196.
Vincent Castronovo1, Philippe Kischel1, François Guillonneau2, Laurence de Leval3, Thierry Deféchereux4, Edwin De Pauw2, Dario Neri5 and David Waltregny1
1 Metastasis Research Laboratory, Center for Experimental Cancer Research, University of Liège, Liège, Belgium
2 Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, Liège, Belgium
3 Department of Pathology, University Hospital of Liège, Liège, Belgium
4 Department of Abdominal Surgery and Transplantation, University Hospital of Liège, Liège, Belgium
5 Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland
DOI: 10.1002/pmic.200600888
2006:
Age-related proteome analysis of the mouse brain: a 2-DE study
Proteomics 2006, 6, 4940-4949. Received February 1, 2006; Revised June 23, 2006; Accepted June 23, 2006.
Odile Carrette1, Pierre R. Burkhard1,2, Denis F. Hochstrasser1,3 and Jean-Charles Sanchez1
1 Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Geneva University, Faculty of Medicine, Geneva, Switzerland
2 Neurology Department, Geneva University Hospital, Geneva, Switzerland
3 Central Clinical Chemistry Laboratory, Geneva University Hospital, Geneva, Switzerland
DOI 10.1002/pmic.200600084
InSilicoSpectro: An Open-Source Proteomics Library
J. Proteome Res.; (Article); 2006; 5(3); 619-624.
Colinge, J.; Masselot, A.; Carbonell, P.; Appel, R. D.
Upper Austria University of Applied Sciences at Hagenberg, Bioinformatics Department, Hauptstrasse 117, A-4232 Hagenberg, Austria.
DOI: 10.1021/pr0504236
Identification of Brain Cell Death Associated Proteins in Human Post-mortem Cerebrospinal Fluid
J. Proteome Res.; (Article); 2006; 5(7); 1674-1681.
Burgess, J. A.; Lescuyer, P.; Hainard, A.; Burkhard, P. R.; Turck, N.; Michel, P.; Rossier, J. S.; Reymond, F.; Hochstrasser, D. F.; Sanchez, J.-C.
Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
DOI: 10.1021/pr060160v
Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers
BMC Genomics 2006, 7:296.
Alexander Scherl1, Patrice François2, Yvan Charbonnier2, Jacques M Deshusses1, Thibaud Koessler2, Antoine Huyghe2, Manuela Bento2, Jianru Stahl-Zeng3, Adrien Fischer2, Alexandre Masselot4, Alireza Vaezzadeh1, Francesca Gallé2, Adriana Renzoni2, Pierre Vaudaux2, Daniel Lew2, Catherine G Zimmermann-Ivol1,5, Pierre-Alain Binz4, Jean-Charles Sanchez1, Denis F Hochstrasser1,5,6 and Jacques Schrenzel2
1 Biomedical Proteomics Research Group, Geneva University, Geneva, Switzerland
2 Service of infectious diseases, University Hospitals of Geneva, Geneva, Switzerland
3 Applied Biosystems, Darmstadt, Germany
4 Geneva Bioinformatics SA, Geneva, Switzerland
5 Central Clinical Chemistry Laboratory, University Hospitals of Geneva, Geneva, Switzerland
6 Pharmacy section, Faculty of Sciences, Geneva University, Geneva, Switzerland
DOI: 10.1186/1471-2164-7-296
Differential Expression Profiling of the Hepatic Proteome in a Rat Model of Dioxin Resistance: CORRELATION WITH GENOMIC AND TRANSCRIPTOMIC ANALYSES
Mol. Cell. Proteomics, May 2006; 5: 882 - 894.
Roberta Pastorelli, Donatella Carpi, Roberta Campagna, Luisa Airoldi, Raimo Pohjanvirta, Matti Viluksela, Helen Hakansson, Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, and Roberto Fanelli
From the Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche "Mario Negri," 20157 Milan, Italy
Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, FIN-00014 Helsinki, Finland
National Veterinary and Food Research Institute and Department of Environmental Health, National Public Health Institute, FIN-70701 Kuopio, Finland
Institute of Environmental Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden
Department of Pharmacology, University of Toronto, Toronto M5S 1A8, Canada
Web-based MS/MS data analysis.
Proteomics. 2006 Sep;6 Suppl 2:22-32.
Lisacek F.
Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
Differential expression of TGFb-stimulated clone 22 in normal prostate and prostate cancer
Int. J. Cancer: 118, 899 - 906 (2006) ' 2005 Wiley-Liss, Inc.
Cyrill A. Rentsch1, Marco G. Cecchini1, Ruth Schwaninger1, Markus Germann1, Regula Markwalder2, Manfred Heller3,Gabri van der Pluijm4, George N. Thalmann1 and Antoinette Wetterwald11 Urology Research Laboratory, Departments of Urology and Clinical Research, University of Bern, Switzerland
2 Institute of Pathology, University of Bern, Switzerland
3 Laboratory for Thrombosis Research, Department of Clinical Research, University of Bern, Switzerland
4 Departments of Endocrinology and Urology, Leiden University Medical Center, Leiden, The Netherlands
2005:
Added Value for Tandem Mass Spectrometry Shotgun Proteomics Data Validation through Isoelectric Focusing of Peptides
J. Proteome Res.; (Article); 2005; 4(6); 2273-2282.
Heller, M.; Ye, M.; Michel, P. E.; Morier, P.; Stalder, D.; Junger, M. A.; Aebersold, R.; Reymond, F.; Rossier, J. S.
DiagnoSwiss SA, Monthey, Switzerland, Department of Clinical Research, University Hospital, 3010 Bern, Switzerland, Institute for Systems Biology, Seattle, Washington 98103, and Institute for Molecular Systems Biology, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland.
DOI: 10.1021/pr050193v
Mass spectrometry-based analytical tools for the molecular protein characterization of human plasma lipoproteins
Proteomics 2005, 5, 2619 - 2630 2619 DOI 10.1002/pmic.200401233
Manfred Heller1, Daniel Stalder1, Evelyn Schlappritzi1, Gertraud Hayn2, Urs Matter2 and André Haeberli1
1 Department of Clinical Research, University Hospital, Bern, Switzerland
2 Comet AG, Analytics, Flamatt, Switzerland
A selection of articles describing the technology behind Phenyx (OLAV):
Experiments in searching small proteins in unannotated large eukaryotic genomes
J Proteome Res. 2005 Jan-Feb;4(1):167-74.
Jacques Colinge, Isabelle Cusin, Samia Reffas, Eve Mahé, Anne Niknejad, Pierre-Andre Rey, H Mattou, M Moniatte, Lydie Bougueleret.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 15707372
Differential proteomics via probabilistic peptide identification scores
Anal Chem. 2005 Jan 15;77(2):596-606.
Colinge J, Chiappe D, Lagache S, Moniatte M., Bougueleret L.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 15649059
High performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics
Proteomics. 2004 Jul;4(7):1977-84
Jacques Colinge, Alexandre Masselot, Isabelle Cusin, Eve Mahé, Anne Niknejad, Guilaine Argoud-Puy, Samia Reffas, N Bederr, Anne Gleizes, Pierre-Andre Rey, Lydie Bougueleret.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 15221758
Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity
DDT: TARGETS, Vol 3, No. 2 (Suppl.), 2004, pp. 50-55.
Jacques Colinge, Alexandre Masselot.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
A systematic statistical analysis of ion trap tandem mass spectra in view of peptide scoring
In: Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), R. Page and G. Benson (Eds), Budapest, September 2003, LNBI 2812, Springer, 25.38, 2003.
Jacques Colinge, Jerome Magnin, Alexandre Masselot.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
OLAV: towards high-throughput tandem mass spectrometry data identification
Proteomics, Vol. 3, No. 8, August 2003, pp. 1454-1463.
Jacques Colinge, Alexandre Masselot, Marc Giron, Thierry Dessingy, Jerome Magnin.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 12923771
Improved peptide charge state assignment
Proteomics, Vol. 3, No. 8, August 2003, pp. 1434-1440.
Jacques Colinge, Jerome Magnin, Thierry Dessingy, Marc Giron, Alexandre Masselot.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 12923768
