Peer Reviewed Publications – Scaffold Software
"A Face in the Crowd: Recognizing Peptides Through Database Search"
Molecular & Cellular Proteomics. 2011 Aug 10: R111.009522.
Jimmy K Eng, Brian C Searle, Karl R Clauser and David L Tabb.
"Protein identification using Sorcerer 2 and SEQUEST"
Curr Protocol Bioinformatics. 2009 Dec;13(13.3).
Martinez Lundgren and Han Wright.
“Proteomic Analysis of Integrin-Associated Complexes Identifies RCC2 as a Dual Regulator Rac1 Arf6”
Sci Signal. 2009 Sept;2(87):ra51.
Jonathan D. Humphries, Adam Byron, Mark D. Bass, Sue E. Craig, John W. Pinney, David Knight, and Martin Humphries
“Extensive fractionation and identification of proteins within nasal lavage fluids from allergic rhinitis and asthmatic chronic rhinosinusitis patients”
J Sep Sci. 2009 Jan;32(1):44-56.
Benson LM, Mason CJ, Friedman O, Kita H, Bergen HR 3rd, Plager DA.
“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
Venkateshwar G. Keshamouni, Pratik Jagtap, George Michailidis, John R. Strahler, Rork Kuick, Ajaya Kumar Reka, Panagiotis Papoulias, Rashmi Krishnapuram, Anjaiah Srirangam, Theodore J. Standiford, Philip C. Andrews and Gilbert S. Omenn
“Chicken egg yolk cytoplasmic proteome, mined via combinatorial peptide ligand libraries”
Journal of Chromatography A Volume 1216, Issue 8, 20 February 2009, Pages 1241-1252
Farinazzo A, Restuccia U, Bachi A, Guerrier L, Fortis F, Boschetti E, Fasoli E, Citterio A, Righetti PG.
“Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated
protein complexes”
Nucleic Acids Research, 2008, Vol. 36, No. 22 6959–6976
“Combining Results from Lectin Affinity Chromatography and Glycocapture Approaches Substantially Improves the Coverage of the Glycoproteome”
Mol Cell Proteomics 2008: 287–301
Claudia A. McDonald, Jane Y. Yang, Vinita Marathe, Ten-Yang Yen, and Bruce A. Macher
“Proteomic analysis of membrane rafts of melanoma cells identifies protein patterns characteristic of the tumor progression stage”
Cell Biology Volume 8 Issue 22, Oct 2008 4733 – 4747
Frédérique Baruthio, Manfredo Quadroni, Curzio Rüegg, Agnese Mariotti, Dr.
“Alterations in protein expression associated with the development of mealiness in peaches”
Journal of Horticultural Science & Biotechnology 2008 83 (1) 85–93
D. M. Obenland,W. H.Vensel and W. J. Hurkman
“Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile”
Journal of Proteome Research 2008, 7, 1027–1035
Sunia A. Trauger, Ewa Kalisak, Jaroslaw Kalisiak, Hirotoshi Morita, Michael V. Weinberg, Angeli Lal Menon, Farris L. Poole II, Michael W. W. Adams, and Gary Siuzdak
“Identification of Fructose-1,6-bisphosphate aldolase cytosolic class I as an NMH7 MADS domain associated protein”
Biochemical and Biophysical Research Communications Volume 376, Issue 4, 28 November 2008, 700-705
Julio Páez-Valencia, Pedro Valencia-Mayoral, Concepción Sánchez-Gómez, Alejandra Contreras-Ramos, Ismael Hernández-Lucas, Eleazar Martínez-Barajas and Alicia Gamboa-deBuen
“Identification of Differentially Expressed Proteins in the Cervical Mucosa of HIV-1-Resistant Sex Workers”
J. Proteome Research 2008, 7 (10), pp 4446–4454
Adam Burgener, Julie Boutilier, Charles Wachihi, Joshua Kimani, Michael Carpenter, Garrett Westmacott, Keding Cheng, Terry B. Ball and Francis Plummer
“Proteomic Analysis of Rat Striatal Synaptosomes during Acrylamide Intoxication at a Low Dose Rate”
Toxicological Sciences 100(1), August, 2007 156–167
David S. Barber, Stanley Stevens, and Richard M. LoPachin
"Intracellular Trafficking of a Polymorphism in the Carboxyl Terminus of the Alpha Subunit of the Human Epithelial Sodium Channel is Modulated by Casein Kinase”
J Am J Physiol Renal Physiol, 2007
Yan, W, Spruce L, Rosenblatt M, Kleyman, T, Rubenstein R,
"Proteomic analysis of cervical-vaginal fluid: identification of novel biomarkers for detection of intra-amniotic infection."
J Proteome Res. 2007 Jan;6(1):89-96.
Gravett MG, Thomas A, Schneider KA, Reddy AP, Dasari S, Jacob T, Lu X, Rodland M, Pereira L, Sadowsky DW, Roberts CT Jr, Novy MJ, Nagalla SR.
"Global Assessment of Regulation of Phosphorylation of Insulin Receptor Substrate-1 by Insulin In Vivo in Human Muscle"
J Diabetes, 56:1508-1516, 2007 Vol. 7, No.3
Yi Z, Langlais P, De Filippis E, Luo M, Flynn C, Schroeder S, Weintraub S, Mapes R, Mandarino L
"Proteomic Analysis of human amniotic fluid"
Molecular & Cellular Proteomics 6:1406-1415, 2007
Chan-Kyung J. Cho, Shannon J. Shan, Elizabeth J. Winsor and Eleftherios P. Diamandis
"Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis "
Molecular & Cellular Proteomics 6:1198-1214, 2007.
Benschop J, Mohammed S, O'Flaherty M, Heck A, Slijper M, Menk F
"Pfnek3 functions as an atypical MAPKK in Plasmodium falciparum "
Biochemical and Biophysical Research Communications Volume 361, Issue 2, 21 September 2007, Pages 439-444
Huiyu Low, Yu Min Lye and Tiow-Suan Sim
"Proteomics Evaluation of Chemically Cleavable Activity-based Probes"
Molecular Cellular Proteomics 6 (10), 1761-70 (01 Oct 2007)
Fonovic M, Verhelst SH, Sorum MT, Bogyo M.
"Proteomic analysis of ovomucoid hypersensitivity in mice by two-dimensional difference gel electrophoresis (2D-DIGE)"
Food and Chemical Toxicology Volume 45, Issue 12, December 2007, Pages 2372-2380
D.J. Hobson, P. Rupa, G.J. Diaz 1, H. Zhang, M. Yang, Y. Mine, P.V. Turner and G.M. Kirby
"Structure-Toxicity Analysis of Type-2 Alkenes: In Vitro Neurotoxicity"
Toxicol. Sci., Jan 2007; 95: 136 - 146.
Richard M. LoPachin, David S. Barber, Brian C. Geohagen, Terrence Gavin, Deke He, and Soma Das
"High copper selectively alters lipid metabolism and cell cycle machinery in the mouse model of Wilson disease "
J. Biol. Chem., Jan 2007; 10.1074/jbc.M607496200.
Dominik Huster, Tina D. Purnat, Jason L. Burkhead, Martina Ralle, Oliver Fiehn, Franziska Stuckert, N. Erik Olson, Daniel Teupser, and Svetlana Lutsenko
"Structure-Toxicity Analysis of Type-2 Alkenes: In Vitro Neurotoxicity "
Toxicological Sciences 2007 95(1):136-146
Richard M. LoPachin, David S. Barber , Brian C. Geohagen, Terrence Gavin, Deke He and Soma Das
"Tandem affinity purification of functional TAP-tagged proteins from human cells"
Nat. Protocols 2 (5), 1145-51 (May 2007)
Juraj Gregan, Christian G Riedel, Mark Petronczki, Lubos Cipak, Cornelia Rumpf, Ina Poser, Frank Buchholz, Karl Mechtler & Kim Nasmyth
"Molecular Cloning and Expression of a cDNA Encoding a Coccidioides posadasii Cu,Zn Superoxide Dismutase Identified by Proteomic Analysis of the Coccidioidal T27K Vaccine"
Annals of the New York Academy of Sciences 1111 (1), 181-97
Lunetta JM, Simmons KA, Johnson SM, Pappagianis D.
"Proteomic analysis of conditioned media from three breast cancer cell lines: A mine for biomarkers and therapeutic targets"
Molecular & Cellular Proteomics 6:1997-2011, 2007.
Vathany Kulasingam and Eleftherios Diamandis
"Endogenous phosphotyrosine signaling in zebrafish embryos"
Molecular Cellular Proteomics, M600482-MCP200 (14 Aug 2007)
Simone M. Lemeer, Rob Ruijtenbeek, Martijn W. H. Pinkse, Chris Jopling, Albert J. R. Heck, Jeroen den Hertog, and Monique Slijper
"Characterization of the human skeletal muscle proteome by one-dimensional Gel electrophoresis and HPLC-ESI-MS/MS"
Molecular Cellular Proteomics, M700304-MCP200 (01 Oct 2007)
Kurt Højlund, Zhengping Yi, Hyonson Hwang, Benjamin Bowen, Natalie Lefort, Charles R. Flynn, Paul Langlais, Susan T. Weintraub, and Lawrence J. Mandarino
"Suction blister fluid as potential body fluid for biomarker proteins"
Proteomics, 7(20) 3638-3650
Jeroen Kool, Léon Reubsaet, Feikje Wesseldijk, Raquel T. Maravilha, Martijn W. Pinkse, Clive S. D'Santos, Jacobus J. van Hilten, Freek J. Zijlstra, Albert J. R. Heck
"Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin"
Molecular Vision 2007; 13:2058-2065
David O. Zamora, Michael Riviere, Dongseok Choi, Yuzhen Pan, Stephen R. Planck, James T. Rosenbaum, Larry L. David, Justine R. Smith
Cannabinoid WIN 55,212-2 Regulates TRPV1 Phosphorylation in Sensory Neurons”</strong
J Bio Chem VOL. 281, NO. 43, pp. 32879–32890, October 27, 2006
Nathaniel A. Jeske, Amol M. Patwardhan, Nikita Gamper, Theodore J. Price, Armen N. Akopian, and Kenneth M. Hargreaves
"Analysis of the cGMP/cAMP Interactome Using a Chemical Proteomics Approach in Mammalian Heart Tissue Validates Sphingosine Kinase Type 1-interacting Protein as Genuine and Highly Abundant AKAP",
J Proteome Res 2006 5, 1435-1447
Scholten A, Poh, MK, van Veen, T, van Breukelen B, Vos M, Heck A
"The Anti-HIV-1 Editing Enzyme APOBEC3G Binds HIV-1 RNA and Messenger RNAs That Shuttle between Polysomes and Stress Granules "
J. Biol. Chem., Sep 2006; 281: 29105 - 29119.
Susan L. Kozak, Mariana Marin, Kristine M. Rose, Cory Bystrom, and David Kabat
"Disease State Differentiation and Identification of Tuberculosis Biomarkers via Native Antigen Array Profiling"
Mol. Cell. Proteomics, Nov 2006; 5: 2102 - 2113.
Todd M. Greco, Roberto Hodara, Ioannis Parastatidis, Harry F. G. Heijnen, Michelle K. Dennehy, Daniel C. Liebler, and Harry Ischiropoulos
"Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells"
PNAS, May 2006; 103: 7420 - 7425.
Mark J. Sartain, Richard A. Slayden, Krishna K. Singh, Suman Laal, and John T. Belisle
"Plasmodium falciparum AMA1 binds a rhoptry neck protein homologous to TgRON4, a component of the moving junction in Toxoplasma gondii."
Eukaryot Cell. 2006 Jul;5(7):1169-73.
Artigues A, Iriarte A, Martinez-Carrion M.
"Identification of Hsc70 binding sites in mitochondrial aspartate aminotransferase."
Arch Biochem Biophys. 2006 Jun 1;450(1):30-8
Alexander DL, Arastu-Kapur S, Dubremetz JF, Boothroyd JC.
"Lumbar Cerebrospinal Fluid Proteome in Multiple Sclerosis: Characterization by Ultrafiltration, Liquid Chromatography, and Mass Spectrometry"
J. Proteome Res.; 2006; 5(7) pp 1647 - 1657
Jean-Paul Noben, Debora Dumont, Natalia Kwasnikowska, Peter Verhaert, Veerle Somers, Raymond Hupperts, Piet Stinissen, and Johan Robben
"Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?"
J Proteome Res. 2006 Oct;5(10):2554-66.
Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL.
"Identification of the moving junction complex of Toxoplasma gondii: a collaboration between distinct secretory organelles."
PLoS Pathog. 2005 Oct;1(2):e17. Epub 2005 Oct 21.
Alexander DL, Mital J, Ward GE, Bradley P, Boothroyd JC.
