Journal Articles Featuring Proteome Software Products

Proteomics Journal Articles

Nuclear import of glucokinase in pancreatic beta-cells is mediated by a nuclear localization
signal and modulated by SUMOylation
Molecular and Cellular Endocrinology (2017)
Bente Berg Johansson, Karianne Fjeld, Marie Holm Solheim, Jun Shirakawa, Enming Zhang, Magdalena Keindl, Jiang Hu, Andreas Lindqvist, Anne Døskeland, Gunnar Mellgren, Torgeir Flatmark, Pål Rasmus Njølstad, Rohit N. Kulkarni, Nils Wierup, Ingvild Aukrust, Lise Bjørkhaug
Molecular and Cellular Endocrinology (2017)

Autoimmune response to transthyretin in juvenile idiopathic arthritis
JCI insight (2016)
Cristina C. Clement, Halima Moncrieffe, Aditi Lele, Ginger Janow, Aniuska Becerra, Francesco Bauli, Fawzy A. Saad, Giorgio Perino, Cristina Montagna, Neil Cobelli, John Hardin, Lawrence J. Stern, Norman Ilowite, Steven A. Porcelli, and Laura Santambrogio
JCI Insight (2016)

Role of carbonyl modifications on aging-associated protein aggregation
Nat. Scientific Reports (2016)
Maya Tanase, Aleksandra M. Urbanska, Valerio Zolla, Cristina C. Clement, Liling Huang, Kateryna Morozova, Carlo Follo, Michael Goldberg, Barbara Roda, Pierluigi Reschiglian and Laura Santambrogio
Nat. Scientific Reports (2016)

Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly
Nat. Cell Biology (2015)
Horton ER, Byron A, Askari JA, Ng DH, Millon-Frémillon A, Robertson J, Koper EJ, Paul NR, Warwood S, Knight D, Humphries JD, Humphries MJ
Nat. Cell Biology (2015)

Genetic background is a key determinant of glomerular extracellular matrix composition and organization
J. of Am. Soc. Nephrology (2015)
Randles MJ, Woolf AS, Huang JL, Byron A, Humphries JD, Price KL, Kolatsi-Joannou M, Collinson S, Denny T, Knight D, Mironov A, Starborg T, Korstanje R, Humphries MJ, Long DA, Lennon R
J. of Am. Soc. Nephrology (2015)

Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling  
Nat. Communications (2015)
Robertson J, Jacquemet G, Byron A, Jones MC, Warwood S, Selley JN, Knight D, Humphries JD, Humphries MJ
Nat. Communications (2015)

A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting
Nat. Communications (2015)
Byron A, Askari JA, Humphries JD, Jacquemet G, Koper EJ, Warwood S, Choi CK, Stroud MJ, Chen CS, Knight D, Humphries MJ.
Nat. Communications (2015)  

Microtubule-dependent modulation of adhesion complex composition
PLoS ONE (2014)
Ng DH, Humphries JD, Byron A, Millon-Frémillon A, Humphries MJ
PLos ONE (2015)

Global analysis reveals the complexity of the human glomerular extracellular matrix
J. of Am. Soc. Nephrology (2014)
Lennon R, Byron A, Humphries JD, Randles MJ, Carisey A, Murphy S, Knight D, Brenchley PE, Zent R, Humphries MJ.
J. of Am. Soc. Nephrology (2015)

Comparison of fractionation strategies post-enrichment by Titania used in the study of the phosphoproteome of a green alga
ABRF Waters Award Poster (2014)
Naldrett M.J., Marsh E.L., Alvarez S. and Evans B.S.
ABRF Waters Award Poster (2015)

Circulating pEGFR is a candidate response biomarker of Cetuximab therapy in colorectal cancer
Clinical Cancer Research (2014)
Katsila T, Juliachs M, Gregori J, Macarulla T, Villarreal L,, Bardelli A, Torrance C, Elez, E, Tabernero J and Villanueva J
Clinical Cancer Research (2014)

Enhancing the biological relevance of secretome-based proteomics by linking tumor cell proliferation and protein secretion
J. of Proteome Research (2014)
Gregori J, Méndez O, Katsila T, Pujals M, Salvans C, Villarreal L, Arribas J, Tabernero J, Sánchez A, Villanueva J
J. of Proteome Research (2014)  

Linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake (Crotalus adamanteus)
J. of Proteomics (2014)
Margres M.J., McGivern J.J., Wray K.P., Seavy M.,Calvin K. and Rokyta D.R.
J. of Proteomics (2014) 

Rac1 is deactivated at integrin activation sites through an IQGAP1-filamin-A-RacGAP1 pathway
J. of Cell Science (2013)
Jacquemet G, Morgan MR, Byron A, Humphries JD, Choi CK, Chen CS, Caswell PT, Humphries MJ
J. of Cell Science (2013)                                                                                         

An effect size filter improves the reproducibility in spectral counting-based comparative proteomics
J. of Proteomics (2013)
Gregori J, Villarreal L, Sánchez A, Baselga J, Villanueva J
J. of Proteomics (2013)   

Proteomic anatomy of human skin
J. of Proteomics (2013)
Leann M. Mikesha, Lavakumar Reddy Aramadhakaa, Christopher Moskalukb, Paola Zigrinoc, Cornelia Mauchc, Jay W. Fox
J. of Proteomics (2013)

Unconventional secretion is a major contributor of cancer cell line secretomes
Mol. Cellular Proteomics (2013)
Villarreal L, Méndez O, Salvans C, Gregori J, Baselga J, Villanueva J
Mol. Cellular Proteomics (2013)

Bovine milk proteome: Quantitative changes in normal milk exosomes, milk fat globule membranes and whey proteomes resulting from Staphylococcus aureus mastitis
J. of Proteomics (2013)
Reinhardt, Timothy A., Randy E. Sacco, Brian J. Nonnecke, and John D. Lippolis
J. of Proteomics (2013) 

Investigating the molecular mechanisms of the interactions between Lactobacillus reuteri strains and intestinal mucus.                  
Thesis submitted for the Degree of Doctor of Philosophy (2012)                                                          
Faye Jeffers, University of East Anglia, Institute of Food Research, Norwich, UK                                   
Thesis submitted for the degree of Doctor of Philosophy   

Batch effects correction improves the sensitivity of significance tests in spectral counting-based comparative discovery proteomics                                                                                              
J. of Proteomics (2012)
Gregori J, Villarreal L, Méndez O, Sánchez A, Baselga J, Villanueva J                                                  
J. of Proteomics (2012) 

Bovine milk exosome proteome  
J. of Proteomics (2012)
Reinhardt, Timothy A., John D. Lippolis, Brian J. Nonnecke, and Randy E. Sacco                                     
J. of Proteomics (2012)

Shotgun proteomics-based clinical testing for diagnosis and classification of amyloidosis
J. of Mass Spectrometry (2013)                                                                                                  
Theis JD, Dasari S, Vrana JA, Kurtin PJ, and Dogan A                                                                        
J. of Mass Spectrometry (2013)                                          

Proteomics of human plasma: A critical comparison of analytical workflows in terms of effort, throughput and outcome
EuPA Open Proteomics (2013)
Dayona L and Kussmanna M                                                                                                      
EuPA Open Proteomics (2013)

Comparative proteomic analysis of supportive and unsupportive extracellular matrix substrates for human embryonic stem cell maintenance                                                                                  
J. of Biol. Chemistry (2013)
Soteriou D, Iskender B, Byron A, Humphries JD, Borg-Bartolo S, Haddock MC, Baxter MA, Knight D, Humphries MJ, Kimber SJ                                                                                                             
J. of Biol. Chemistry (2013)  

Proteomic analysis of extracellular matrix from the hepatic stellate cell line LX-2 identifies CYR61 and Wnt-5a as novel constituents of fibrotic liver                                                                        
J. of Proteome Research (2012)
Rashid ST, Humphries JD, Byron A, Dhar A, Askari JA, Selley JN, Knight D, Goldin RD, Thursz M, Humphries MJ                                                                                              
J. of Proteome Research (2012)

Proteomic analysis of α4β1 integrin adhesion complexes reveals α-subunit-dependent protein recruitment
Proteomics (2012)
Byron A, Humphries JD, Bass MD, Knight D, Humphries MJ                                                                 
Proteomics (2012)  
 

Effects of space flight on the expression of liver proteins in the mouse
J. of Proteomics & Bioinformatics (2012)                                                                                  
Gridley DS, Pecaut MJ, Green LM, Herrmann EC, Bianski B, Slater JM, Stodieck LS, Ferguson VL and Sandberg LB                                                                                                                             
J. of Proteomics & Bioinformatics (2012)

A face in the crowd: Recognizing peptides through database search
Mol. Cellular Proteomics (2011)
Jimmy K Eng, Brian C Searle, Karl R Clauser and David L Tabb                                                            
Mol. Cellular Proteomics (2011)

Proteomic analysis of integrin adhesion complexes
Sci. Signaling (2011)
Byron A, Humphries JD, Bass MD, Knight D, Humphries MJ
Sci. Signaling (2011) 

Protein identification using Sorcerer 2 and Sequest
Curr. Protoc. Bioinformatics (2009)                                                                                                
Martinez Lundgren and Han Wright                                                                                                
Curr. Protoc. Bioinformatics (2009)

Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator Rac1 Arf6
Sci. Signaling (2009)
Jonathan D. Humphries, Adam Byron, Mark D. Bass, Sue E. Craig, John W. Pinney, David Knight, and Martin Humphries
Sci. Signaling (2009)

Extensive fractionation and identification of proteins within nasal lavage fluids from allergic rhinitis and asthmatic chronic rhinosinusitis patients
J. of Sep. Science (2009)
Benson LM, Mason CJ, Friedman O, Kita H, Bergen HR 3rd, Plager DA
J. of Sep. Science (2009)

Pathway-based biomarker search by high-throughput proteomics profiling of secretomes
J. of Proteome Research (2009)
Lawlor K, Nazarian A, Lacomis L, Tempst P, Villanueva J*
J. of Proteome Research (2009)

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. of Proteome Research (2009)
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
J. of Proteome Research (2009) 

Chicken egg yolk cytoplasmic proteome, mined via combinatorial peptide ligand libraries
J. of Chromatography (2009)
Farinazzo A, Restuccia U, Bachi A, Guerrier L, Fortis F, Boschetti E, Fasoli E, Citterio A, Righetti PG
J. of Chromatography (2009) 

Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes
Nucleic Acids Research (2008)
Jean-Philippe Gagné, Maxim Isabelle, Ken Sin Lo, Sylvie Bourassa, Michael J. Hendzel, Valina L. Dawson, Ted M. Dawson and Guy G. Poirier
Nucleic Acids Research (2008)

Combining results from lectin affinity chromatography and glycocapture approaches substantially improves the coverage of the glycoproteome
Mol. Cell Proteomics (2008)
Claudia A. McDonald, Jane Y. Yang, Vinita Marathe, Ten-Yang Yen, and Bruce A. Macher
Mol. Cell Proteomics (2008)

Proteomic analysis of membrane rafts of melanoma cells identifies protein patterns characteristic of the tumor progression stage
Cell Biology (2008)
Frédérique Baruthio, Manfredo Quadroni, Curzio Rüegg, Agnese Mariotti, Dr.
Cell Biology (2008)    

Alterations in protein expression associated with the development of mealiness in peaches
J. of Horticultural Sciences & Biotechnology (2008)
D. M. Obenland,W. H.Vensel and W. J. Hurkman
J. of Horticultural Sciences & Biotechnology (2008)

Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile
J. of Proteome Research (2008)
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 Siuzdaz
J. of Proteome Research (2008) 

Identification of fructose-1,6-bisphosphate aldolase cytosolic class I as an NMH7 MADS domain associated protein
Biochemical & Biophysical Research Communications (2008)
Julio Páez-Valencia, Pedro Valencia-Mayoral, Concepción Sánchez-Gómez, Alejandra Contreras-Ramos, Ismael Hernández-Lucas, Eleazar Martínez-Barajas and Alicia Gamboa-deBuen
Biochemical & Biophysical Research Communications (2008)

Identification of differentially expressed proteins in the cervical mucosa of HIV-1-resistant sex workers
J. of Proteome Research (2008)
Adam Burgener, Julie Boutilier, Charles Wachihi, Joshua Kimani, Michael Carpenter, Garrett Westmacott, Keding Cheng, Terry B. Ball and Francis Plummer
J. of Proteome Research (2008)

Proteomic analysis of rat striatal synaptosomes during acrylamide intoxication at a low dose rate
Toxicological Sciences (2008)
David S. Barber, Stanley Stevens, and Richard M. LoPachin
Toxicological Sciences (2008)

Intracellular trafficking of a polymorphism in the carboxyl terminus of the alpha subunit of the human epithelial sodium channel is modulated by casein kinase
Am. Journal of Physiology: Renal Physiology (2007)
Yan, W, Spruce L, Rosenblatt M, Kleyman, T, Rubenstein R
Am. Journal of Physiology: Renal Physiology (2008)  

Proteomic analysis of cervical-vaginal fluid: identification of novel biomarkers for detection of intra-amniotic infection
J. of Proteome Research (2007)
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.
J. of Proteome Research (2007)

Global assessment of regulation of phosphorylation of insulin receptor substrate-1 by insulin in vivo in human muscle
J. of Diabetes (2007)
Yi Z, Langlais P, De Filippis E, Luo M, Flynn C, Schroeder S, Weintraub S, Mapes R, Mandarino L
J. of Diabetes (2007)  

Proteomic analysis of human amniotic fluid
Mol. Cellular Proteomics (2007)
Chan-Kyung J. Cho, Shannon J. Shan, Elizabeth J. Winsor and Eleftherios P. Diamandis
Mol. Cellular Proteomics (2007)

Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis
Mol. Cellular Proteomics (2007)
Benschop J, Mohammed S, O'Flaherty M, Heck A, Slijper M, Menk F
Mol. Cellular Proteomics (2007)

Pfnek3 functions as an atypical MAPKK in Plasmodium falciparum
Biochemical & Biophysical Research Communications (2007)
Huiyu Low, Yu Min Lye and Tiow-Suan Sim
Biochemical & Biophysical Research Communications (2007)

Proteomics evaluation of chemically cleavable activity-based probes
Mol. Cellular Proteomics (2007)
Fonovic M, Verhelst SH, Sorum MT, Bogyo M.
Mol. Cellular Proteomics (2007) 

Proteomic analysis of ovomucoid hypersensitivity in mice by two-dimensional difference gel electrophoresis (2D-DIGE)
Food & Chemical Toxicology (2007)
D.J. Hobson, P. Rupa, G.J. Diaz 1, H. Zhang, M. Yang, Y. Mine, P.V. Turner and G.M. Kirby
Food & Chemical Toxicology (2007)

Structure-toxicity analysis of type-2 alkenes: in vitro neurotoxicity
Toxicological Sci. (2007)
Richard M. LoPachin, David S. Barber, Brian C. Geohagen, Terrence Gavin, Deke He, and Soma Das
Toxicological Sci. (2007)

High copper selectively alters lipid metabolism and cell cycle machinery in the mouse model of Wilson disease
J. of Biol. Chemistry (2007)
Dominik Huster, Tina D. Purnat, Jason L. Burkhead, Martina Ralle, Oliver Fiehn, Franziska Stuckert, N. Erik Olson, Daniel Teupser, and Svetlana Lutsenko
J. of Biol. Chemistry (2007)

Tandem affinity purification of functional TAP-tagged proteins from human cells
Nat. Protocols (2007)
Juraj Gregan, Christian G Riedel, Mark Petronczki, Lubos Cipak, Cornelia Rumpf, Ina Poser, Frank Buchholz, Karl Mechtler & Kim Nasmyth
Nat. Protocols (2007)

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 NY Academy of Sciences (2007)
Lunetta JM, Simmons KA, Johnson SM, Pappagianis D.
Annals of the NY Academy of Sciences (2007)

Proteomic analysis of conditioned media from three breast cancer cell lines: A mine for biomarkers and therapeutic targets
Mol. Cellular Proteomics (2007)
Vathany Kulasingam and Eleftherios Diamandis
Mol. Cellular Proteomics (2007)   

Endogenous phosphotyrosine signaling in zebrafish embryos
Mol. Cellular Proteomics (2007)
Simone M. Lemeer, Rob Ruijtenbeek, Martijn W. H. Pinkse, Chris Jopling, Albert J. R. Heck, Jeroen den Hertog, and Monique Slijper
Mol. Cellular Proteomics (2007)  

Characterization of the human skeletal muscle proteome by one-dimensional gel electrophoresis and HPLC-ESI-MS/MS
Mol. Cellular Proteomics (2007)
Kurt Højlund, Zhengping Yi, Hyonson Hwang, Benjamin Bowen, Natalie Lefort, Charles R. Flynn, Paul Langlais, Susan T. Weintraub, and Lawrence J. Mandarino
Mol. Cellular Proteomics (2007)

Suction blister fluid as potential body fluid for biomarker proteins
Proteomics (2007)
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.
Proteomics (2007)

Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin
Mol. Vision (2007)
David O. Zamora, Michael Riviere, Dongseok Choi, Yuzhen Pan, Stephen R. Planck, James T. Rosenbaum, Larry L. David, Justine R. Smith
Mol. Vision (2007)   

Cannabinoid WIN 55,212-2 regulates TRPV1 phosphorylation in sensory neurons
J. of Biol. Chemistry (2006)
Nathaniel A. Jeske, Amol M. Patwardhan, Nikita Gamper, Theodore J. Price, Armen N. Akopian, and Kenneth M. Hargreaves
J. of Biol. Chemistry (2006)

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. of Proteome Research (2006)
Scholten A, Poh, MK, van Veen, T, van Breukelen B, Vos M, Heck A
J. of Proteome Research (2006)  

The anti-HIV-1 editing enzyme APOBEC3G binds HIV-1 RNA and messenger RNAs that shuttle between polysomes and stress granules
J. of Biol. Chemistry (2006)
Susan L. Kozak, Mariana Marin, Kristine M. Rose, Cory Bystrom, and David Kabat
J. of Biol. Chemistry (2006)

Disease state differentiation and identification of Tuberculosis biomarkers via native antigen array profiling
Mol. Cellular Proteomics (2006)
Todd M. Greco, Roberto Hodara, Ioannis Parastatidis, Harry F. G. Heijnen, Michelle K. Dennehy, Daniel C. Liebler, and Harry Ischiropoulos
Mol. Cellular Proteomics (2006) 

Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells
PNAS (2006)
Mark J. Sartain, Richard A. Slayden, Krishna K. Singh, Suman Laal, and John T. Belisle
PNAS (2006)

Plasmodium falciparum AMA1 binds a rhoptry neck protein homologous to TgRON4, a component of the moving junction in Toxoplasma gondii
Eukaryotic Cell (2006)
Artigues A, Iriarte A, Martinez-Carrion M.
Eukaryotic Cell (2006)

Identification of Hsc70 binding sites in mitochondrial aspartate aminotransferase
Archives of Biochemistry & Biophysics (2006)
Alexander DL, Arastu-Kapur S, Dubremetz JF, Boothroyd JC.
Archives of Biochemistry & Biophysics (2006)

Lumbar cerebrospinal fluid proteome in Multiple Sclerosis: Characterization by ultrafiltration, liquid chromatography, and mass spectrometry
J. of Proteome Research (2006)
Jean-Paul Noben, Debora Dumont, Natalia Kwasnikowska, Peter Verhaert, Veerle Somers, Raymond Hupperts, Piet Stinissen, and Johan Robben
J. of Proteome Research (2006)

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. of Proteome Research (2006)
Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL.
J. of Proteome Research (2006)

Identification of the moving junction complex of Toxoplasma gondii: A collaboration between distinct secretory organelles
PLoS Pathology (2005)
Alexander DL, Mital J, Ward GE, Bradley P, Boothroyd JC.
PLoS Pathology (2005)

Metabolomics Journal Articles 

A relative quantitative positive/negative ion switching method for untargeted lipidomics via
high resolution LC-MS/MS from any biological source
Metabolomics (2017)
Susanne B. Breitkopf, Stéphane J. H. Ricoult, Min Yuan, Ying Xu, David A. Peake, Brendan D. Manning, John M. Asara
Metabolomics (2017)

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