|
SPS' DigestIssue 61, 12-Jun-2009 |
LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia
Frohlich T, Arnold GJ, Fritsch R, Mayr T, Laforsch C.
BMC Genomics (2009) 10(1): 171
Proteome coverage prediction with infinite Markov models
Manfred Claassen, Ruedi Aebersold, and Joachim M. Buhmann
Bioinformatics (2009) 25(12): i154-i160
Database interrogation algorithms for identification of proteins in proteomic separations
Palagi PM, Lisacek F, Appel RD.
Methods Mol Biol (2009) 519: 515-31
Prediction of Linear B-cell Epitopes
Reimer U.
Methods Mol Biol (2009) 524: 335-44
RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information
Rakesh Kaundal, Gajendra P. S. Raghava
PROTEOMICS (2009) 9(9): 2324-2342
GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models
Frederic Y. Bois
Bioinformatics (2009) 25(11): 1453-1454
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, and Michiel J. L. de Hoon
Bioinformatics (2009) 25(11): 1422-1423
On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm
Herbert Oberacher, Marion Pavlic, Kathrin Libiseller, Birthe Schubert, Michael Sulyok, Rainer Schuhmacher, Edina Csaszar, Harald C. Köfeler
Journal of Mass Spectrometry (2009) 44(4): 494-502
SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid
Andreas Quandt, Alexandre Masselot, Patricia Hernandez, Céline Hernandez, Sergio Maffioletti, Ron D. Appel, Frederique Lisacek
PROTEOMICS (2009) 9(10): 2648-2655
Statistical Model to Analyze Quantitative Proteomics Data Obtained by 18O/16O Labeling and Linear Ion Trap Mass Spectrometry: Application to the Study of Vascular Endothelial Growth Factor-induced Angiogenesis in Endothelial Cells
Inmaculada Jorge, Pedro Navarro, Pablo Martinez-Acedo, Estefania Nunez, Horacio Serrano, Arantzazu Alfranca, Juan Miguel Redondo, and Jesus Vazquez
Mol Cell Proteomics (2009) 8(5): 1130-1149
A retention-time-shift-tolerant background subtraction and noise reduction algorithm (BgS-NoRA) for extraction of drug metabolites in liquid chromatography/mass spectrometry data from biological matrices
Peijuan Zhu, Wei Ding, Wei Tong, Anima Ghosal, Kevin Alton, Swapan Chowdhury
Rapid Communications in Mass Spectrometry (2009) 23(11): 1563-1572
Automated diagnosis of LC-MS/MS performance
Hua Xu and Michael A. Freitas
Bioinformatics (2009) 25(10): 1341-1343
A strategy for the prior processing of high-resolution mass spectral data obtained from high-dimensional combined fractional diagonal chromatography
Dirk Valkenborg, Grégoire Thomas, Luc Krols, Koen Kas, Tomasz Burzykowski
Journal of Mass Spectrometry (2009) 44(4): 516-529
Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods
Leversen NA, De Souza GA, MÃ¥len H, Prasad S, Jonassen I, Wiker HG.
Microbiology Early Edition: published 23-Apr-2009
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin, David M. Kristensen, and Olivier Lichtarge
Bioinformatics (2009) 25(11): 1426-1427
Protein sumoylation sites prediction based on two-stage feature selection
Lu L, Shi XH, Li SJ, Xie ZQ, Feng YL, Lu WC, Li YX, Li H, Cai YD.
Mol Divers Early Edition: published 27-May-2009
Studying the effects of correlation on protein selection in proteomics data
Savita Venkataramani, Dayanand N. Naik
PROTEOMICS (2009) 9(10): 2883-2887
Experimental annotation of channel catfish virus by probabilistic proteogenomic mapping
Dusan Kunec, Bindu Nanduri, Shane C. Burgess
PROTEOMICS (2009) 9(10): 2634-2647
Is bagging effective in the classification of small-sample genomic and proteomic data?
Vu TT, Braga-Neto UM.
EURASIP J Bioinform Syst Biol (2009) : 158368.
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
Cox J, Matic I, Hilger M, Nagaraj N, Selbach M, Olsen JV, Mann M.
Nat Protoc (2009) 4(5): 698-705
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Eric L. Peterson, Jane Kondev, Julie A. Theriot, and Rob Phillips
Bioinformatics (2009) 25(11): 1356-1362
Computational biology for cardiovascular biomarker discovery
Francisco Azuaje, Yvan Devaux, and Daniel Wagner
Brief Bioinform (2009) 10(4): 367-377
MitoMiner, an Integrated Database for the Storage and Analysis of Mitochondrial Proteomics Data
Anthony C. Smith and Alan J. Robinson
Mol Cell Proteomics (2009) 8(6): 1324-1337
Troubleshooting Image Analysis in 2DE
Levänen B, Wheelock AM.
Methods Mol Biol (2009) 519: 111-128
MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields
Xuefeng Xia, Song Zhang, Yu Su, and Zhirong Sun
Bioinformatics (2009) 25(11): 1433-1434
PPI spider: A tool for the interpretation of proteomics data in the context of protein-protein interaction networks
Alexey V. Antonov, Sabine Dietmann, Igor Rodchenkov, Hans W. Mewes
PROTEOMICS (2009) 9(10): 2740-2749
StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry
Bas van Breukelen, Henk W. P. van den Toorn, Madalina M. Drugan, and Albert J. R. Heck
Bioinformatics (2009) 25(11): 1472-1473
Creating 2DE Databases for the World Wide Web
Hoogl C, Mostaguir K, Appel RD.
Methods Mol Biol (2009) 519: 533-9
Predicting liquid chromatographic retention times of peptides from the Drosophila melanogaster proteome by machine learning approaches
Tian F, Yang L, Lv F, Zhou P.
Anal Chim Acta (2009) 644(1-2): 10-6
Inferring protein-protein interactions from multiple protein domain combinations
Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA.
Methods Mol Biol (2009) 541: 1-17
Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification
Sangtae Kim, Nuno Bandeira, and Pavel A. Pevzner
Mol Cell Proteomics (2009) 8(6): 1391-1400
In Silico Analysis of Phosphoproteome Data Suggests a Rich-get-richer Process of Phosphosite Accumulation over Evolution
Nozomu Yachie, Rintaro Saito, Junichi Sugahara, Masaru Tomita, and Yasushi Ishihama
Mol Cell Proteomics (2009) 8(5): 1061-1071
Variable slope normalization of reverse phase protein arrays
E. Shannon Neeley, Steven M. Kornblau, Kevin R. Coombes, and Keith A. Baggerly
Bioinformatics (2009) 25(11): 1384-1389
SBML2LATEX: Conversion of SBML files into human-readable reports
Andreas Drager, Hannes Planatscher, Dieudonne Motsou Wouamba, Adrian Schroder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Muller, and Andreas Zell
Bioinformatics (2009) 25(11): 1455-1456
Integrating shotgun proteomics and mRNA expression data to improve protein identification
Smriti R. Ramakrishnan, Christine Vogel, John T. Prince, Zhihua Li, Luiz O. Penalva, Margaret Myers, Edward M. Marcotte, Daniel P. Miranker, and Rong Wang
Bioinformatics (2009) 25(11): 1397-1403
Excretory/Secretory Proteome of the Adult Developmental Stage of Human Blood Fluke, Schistosoma japonicum
Feng Liu, Shu-Jian Cui, Wei Hu, Zheng Feng, Zhi-Qin Wang, and Ze-Guang Han
Mol Cell Proteomics (2009) 8(6): 1236-1251
Proteomics of MUC1-containing lipid rafts from plasma membranes and exosomes of human breast carcinoma cells MCF-7
Simon Staubach, Hanieh Razawi, Franz-Georg Hanisch
PROTEOMICS (2009) 9(10): 2820-2835
Fitness of Escherichia coli during Urinary Tract Infection Requires Gluconeogenesis and the TCA Cycle
Alteri CJ, Smith SN, Mobley HL.
PLoS Pathog (2009) 5(5): e1000448
Proteomic analysis of fungal host factors differentially expressed by Fusarium graminearum infected with virus strain DK21
Kwon SJ, Cho SY, Lee KM, Yu J, Sohn MI, Kim KH.
Virus Res Early Edition: published 14-Apr-2009
Microsomal Proteomics
Wong DM, Adeli K.
Methods Mol Biol (2009) 519: 273-289
A comprehensive proteome map of the Haemophilus parasuis serovar 5
Mingguang Zhou, Anding Zhang, Yi Guo, Yonghong Liao, Huanchun Chen, Meilin Jin
PROTEOMICS (2009) 9(10): 2722-2739
An attempt to understand kidney's protein handling function by comparing plasma and urine proteomes
Jia L, Zhang L, Shao C, Song E, Sun W, Li M, Gao Y.
PLoS ONE (2009) 4(4): e5146
Differential protein expression in Corbicula fluminea upon exposure to a Microcystis aeruginosa toxic strain
Martins JC, Leão PN, Vasconcelos V.
Toxicon Early Edition: published 13-Jan-2009
Differential Permeabilization Effects of Ca2+ and Valinomycin on the Inner and Outer Mitochondrial Membranes as Revealed by Proteomics Analysis of Proteins Released from Mitochondria
Akiko Yamada, Takenori Yamamoto, Naoshi Yamazaki, Kikuji Yamashita, Masatoshi Kataoka, Toshihiko Nagata, Hiroshi Terada, and Yasuo Shinohara
Mol Cell Proteomics (2009) 8(6): 1265-1277
Identification and cell cycle-dependent localization of nine novel, genuine centrosomal components in Dictyostelium discoideum
Schulz I, Erle A, Gräf R, Krüger A, Lohmeier H, Putzler S, Samereier M, Weidenthaler S.
Cell Motil Cytoskeleton Early Edition: published 22-May-2009
Proteomic assessment of caffeine effects on coral symbionts
Pollack K, Balazs K, Ogunseitan O.
Environ Sci Technol (2009) 43(6): 2085-91
Acclimatory responses of the Daphnia pulex proteome to environmental changes. II. Chronic exposure to different temperatures (10 and 20 degrees C) mainly affects protein metabolism
Schwerin S, Zeis B, Lamkemeyer T, Paul RJ, Koch M, Madlung J, Fladerer C, Pirow R.
BMC Physiol (2009) 9(1): 8
The algal metabolite yessotoxin affects heterogeneous nuclear ribonucleoproteins in HepG2 cells
Clifford Young, Penelope Truman, Magalie Boucher, Robert A. Keyzers, Peter Northcote, T. William Jordan
PROTEOMICS (2009) 9(9): 2529-2542
Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis
Pannekoek Y, Huis In 't Veld R, Hopman CT, Langerak AA, Speijer D, van der Ende A.
FEMS Microbiol Lett (2009) 294(2): 216-24
Cgr11 encodes a secretory protein involved in cell adhesion
Devnath S, Kataoka T, Miura K, Kusuda M, Kitamura K, Kumada Y, Mochiduki A, Kaneko K, Adachi A, Inoue K.
Eur J Cell Biol Early Edition: published 26-May-2009
Selectivity in Enrichment of cAMP-dependent Protein Kinase Regulatory Subunits Type I and Type II and Their Interactors Using Modified cAMP Affinity Resins
Thin Thin Aye, Shabaz Mohammed, Henk W. P. van den Toorn, Toon A. B. van Veen, Marcel A. G. van der Heyden, Arjen Scholten, and Albert J. R. Heck
Mol Cell Proteomics (2009) 8(5): 1016-1028
Proteomic analysis of parthenogenetic and in vitro fertilized porcine embryos
Mukesh Kumar Gupta, Jung Mi Jang, Jin Woo Jung, Sang Jun Uhm, Kwang Pyo Kim, Hoon Taek Lee
PROTEOMICS (2009) 9(10): 2846-2860
The Organelle Proteome of the DT40 Lymphocyte Cell Line
Stephanie L. Hall, Svenja Hester, Julian L. Griffin, Kathryn S. Lilley, and Antony P. Jackson
Mol Cell Proteomics (2009) 8(6): 1295-1305
Protein Profiles in Zebrafish (Danio rerio) Embryos Exposed to PFOS
Shi X, Yeung LW, Lam PK, Wu RS, Zhou B.
Toxicol Sci Early Edition: published 27-May-2009
2D-DIGE: Comparative Proteomics of Cellular Signalling Pathways
Larbi NB, Jefferies C.
Methods Mol Biol (2009) 517: 1-28
RNF2 is the target for phosphorylation by the p38 MAPK and ERK signaling pathways
Prema S. Rao, Arun Satelli, Sheng Zhang, Sanjay K. Srivastava, Kalkunte S. Srivenugopal, U. Subrahmanyeswara Rao
PROTEOMICS (2009) 9(10): 2776-2787
Embryonic stem cells derived from somatic cloned and fertilized blastocysts are post-transcriptionally indistinguishable: A MicroRNA and protein profile comparison
Junjun Ding, Yuanbiao Guo, Sheng Liu, Yujuan Yan, Gang Chang, Zhaohui Kou, Yu Zhang, Ying Jiang, Fuchu He, Shaorong Gao, Jianli Sang
PROTEOMICS (2009) 9(10): 2711-2721
Chromatographic and electrophoretic resolution of proteins and protein complexes from the larval midgut microvilli of Manduca sexta
Pauchet Y, Muck A, Svatoš A, Heckel DG.
Insect Biochem Mol Biol Early Edition: published 21-May-2009
Adrenaline and reactive oxygen species elicit proteome and energetic metabolism modifications in freshly isolated rat cardiomyocytes
Costa VM, Silva R, Tavares LC, Vitorino R, Amado F, Carvalho F, Bastos Mde L, Carvalho M, Carvalho RA, Remião F.
Toxicology (2009) 260(1-3): 84-96
The Depressive Phenotype Induced in Adult Female Rats by Adolescent Exposure to THC is Associated with Cognitive Impairment and Altered Neuroplasticity in the Prefrontal Cortex
Rubino T, Realini N, Braida D, Alberio T, Capurro V, Viganò D, Guidali C, Sala M, Fasano M, Parolaro D.
Neurotox Res (2009) 15(4): 291-302
Proteomic Analysis of Caenorhabditis elegans
Jeong PY, Na K, Jeong MJ, Chitwood D, Shim YH, Paik YK.
Methods Mol Biol (2009) 519: 145-169
Proteomics and Pathway Analysis Identifies JNK Signaling as Critical for High Linear Energy Transfer Radiation-induced Apoptosis in Non-small Lung Cancer Cells
Sara Stahl, Eva Fung, Christopher Adams, Johan Lengqvist, Birgitta Mork, Bo Stenerlow, Rolf Lewensohn, Janne Lehtio, Roman Zubarev, and Kristina Viktorsson
Mol Cell Proteomics (2009) 8(5): 1117-1129
Proteomic analysis of protein complexes in toll-like receptor biology
Brennan K, Jefferies CA.
Methods Mol Biol (2009) 517: 1-14
Distinct contractile and cytoskeletal protein patterns in the Antarctic midge are elicited by desiccation and rehydration
Aiqing Li, Joshua B. Benoit, Giancarlo Lopez-Martinez, Michael A. Elnitsky, Richard E. Lee Jr, David L. Denlinger
PROTEOMICS (2009) 9(10): 2788-2798
Diabetic dyslipidemia and exercise alter the plasma low-density lipoproteome in Yucatan pigs
Matthew R. Richardson, Xianyin Lai, Joseph L. Dixon, Michael Sturek, Frank A. Witzmann
PROTEOMICS (2009) 9(9): 2468-2483
Detection of growth hormone responsive proteins using SELDI-TOF mass spectrometry
Chung L, Baxter RC.
Growth Horm IGF Res Early Edition: published 23-May-2009
Organelle proteomics
Plöscher M, Granvogl B, Reisinger V, Masanek A, Eichacker LA.
Methods Mol Biol (2009) 519: 65-82
Proteomic analysis of the phytopathogenic fungus Botrytis cinerea during cellulose degradation
Francisco Javier Fernández-Acero, Thomas Colby, Anne Harzen, Jesús Manuel Cantoral, Jürgen Schmidt
PROTEOMICS (2009) 9(10): 2892-2902
LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia
Frohlich T, Arnold GJ, Fritsch R, Mayr T, Laforsch C.
BMC Genomics (2009) 10(1): 171
Identification and characterization of proteins interacting with SIRT1 and SIRT3: implications in the anti-aging and metabolic effects of sirtuins
Ivy K. M. Law, Ling Liu, Aimin Xu, Karen S. L. Lam, Paul M. Vanhoutte, Chi-Ming Che, Priscilla T. Y. Leung, Yu Wang
PROTEOMICS (2009) 9(9): 2444-2456
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Quantitative Comparison of the Membrane Proteomes of Self-renewing and Differentiating Human Embryonic Stem Cells
Tatyana A. Prokhorova, Kristoffer T. G. Rigbolt, Pia T. Johansen, Jeanette Henningsen, Irina Kratchmarova, Moustapha Kassem, and Blagoy Blagoev
Mol Cell Proteomics (2009) 8(5): 959-970
Comparative proteome analysis of the Aspergillus fumigatus mutant deficient of glucosidase I (AfCwh41)
Zhang L, Feng D, Fang W, Ouyang H, Luo Y, Du T, Jin C.
Microbiology Early Edition: published 23-Apr-2009
Electron transfer protein complexes in the thylakoid membranes of heterocysts from the cyanobacterium Nostoc punctiforme
Cardona T, Battchikova N, Zhang P, Stensjö K, Aro EM, Lindblad P, Magnuson A.
Biochim Biophys Acta (2009) 1787(4): 252-63
Comparative Proteomic Analysis of Tolerance and Adaptation of Ethanologenic Yeast to Furfural, a Lignocellulosic Inhibitory Compound
Lin FM, Qiao B, Yuan YJ.
Appl Environ Microbiol (2009) 75(11): 3765-76
MMP-9 Sheds the {beta}2 Integrin Subunit (CD18) from Macrophages
Tomas Vaisar, Sean Y. Kassim, Ivan G. Gomez, Pattie S. Green, Sara Hargarten, Peter J. Gough, William C. Parks, Carole L. Wilson, Elaine W. Raines, and Jay W. Heinecke
Mol Cell Proteomics (2009) 8(5): 1044-1060
Cell-Based Identification of Natural Substrates and Cleavage Sites for Extracellular Proteases by SILAC Proteomics
Gioia M, Foster LJ, Overall CM.
Methods Mol Biol (2009) 539: 1-23
Mammalian epididymal proteome
Dacheux JL, Belleannée C, Jones R, Labas V, Belghazi M, Guyonnet B, Druart X, Gatti JL, Dacheux F.
Mol Cell Endocrinol (2009) 306(1-2): 45-50
Quantitative detection of changes in the leaf-mesophyll tonoplast proteome in dependency of a cadmium exposure of barley (Hordeum vulgare L.) plants
Thomas Schneider, Maja Schellenberg, Stefan Meyer, Felix Keller, Peter Gehrig, Kathrin Riedel, Youngsook Lee, Leo Eberl, Enrico Martinoia
PROTEOMICS (2009) 9(10): 2668-2677
Proteome profile of the mature rat olfactory bulb
Devendra Kumar Maurya, Curam Sreenivasacharlu Sundaram, Purnima Bhargava
PROTEOMICS (2009) 9(9): 2593-2599
Biochemical and proteomic effects in Procambarus clarkii after chlorpyrifos or carbaryl exposure under sublethal conditions
Vioque-Fernández A, de Almeida EA, López-Barea J.
Biomarkers Early Edition: published 1-Jun-2009
Proteomic analysis of hybrid poplar xylem sap
Dafoe NJ, Constabel CP.
Phytochemistry Early Edition: published 23-May-2009
The genome and proteome of a virulent Escherichia coli O157:H7 bacteriophage closely resembling Salmonella phage Felix O1
Villegas A, She YM, Kropinski AM, Lingohr EJ, Mazzocco A, Ojha S, Waddell TE, Ackermann HW, Moyles DM, Ahmed R, Johnson RP.
Virol J (2009) 6(1): 41
First evidence of a membrane-bound, tyramine and ?-phenylethylamine producing, tyrosine decarboxylase in Enterococcus faecalis: A two-dimensional electrophoresis proteomic study
Enrica Pessione, Alessandro Pessione, Cristina Lamberti, Daniel Jean Coïsson, Kathrin Riedel, Roberto Mazzoli, Silvia Bonetta, Leo Eberl, Carlo Giunta
PROTEOMICS (2009) 9(10): 2695-2710
Identification of major royal jelly proteins in the brain of the honeybee Apis mellifera
Peixoto LG, Calábria LK, Garcia L, Capparelli FE, Goulart LR, Sousa MV, Espindola FS.
J Insect Physiol Early Edition: published 19-May-2009
Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments
Benndorf D, Vogt C, Jehmlich N, Schmidt Y, Thomas H, Woffendin G, Shevchenko A, Richnow HH, von Bergen M.
Biodegradation Early Edition: published 21-Apr-2009
Protein identification and mRNA analysis of phytochrome-regulated genes in Arabidopsis under red light
Li X, Yang Y, Li Y, Wang J, Xiao X, Guo X, Tang D, Liu X.
Sci China C Life Sci (2009) 52(4): 371-80
Proteomic analysis of chicory root identifies proteins typically involved in cold acclimation
Hervé Degand, Anne-Marie Faber, Nicolas Dauchot, Dominique Mingeot, Bernard Watillon, Pierre Van Cutsem, Pierre Morsomme, and Marc Boutry
PROTEOMICS (2009) 9(10): 2903-2907
Proteomic analysis of the adaptive response of Salmonella enterica serovar Typhimurium to growth under anaerobic conditions
Encheva V, Shah HN, Gharbia SE.
Microbiology Early Edition: published 23-Apr-2009
Effects of Typical (Haloperidol) and Atypical (Risperidone) Antipsychotic Agents on Protein Expression in Rat Neural Stem Cells
Kashem MA, Ummehany R, Ukai W, Hashimoto E, Saito T, McGregor IS, Matsumoto I.
Neurochem Int Early Edition: published 19-May-2009
Proteomics and human embryonic stem cells
Van Hoof D, Heck AJ, Krijgsveld J, Mummery CL.
Stem Cell Res (2008) 1(3): 169-82
Understanding rice plant resistance to the Brown Planthopper (Nilaparvata lugens): A proteomic approach
Zhe Wei, Wei Hu, Qishan Lin, Xiaoyan Cheng, Mengjie Tong, Lili Zhu, Rongzhi Chen, Guangcun He
PROTEOMICS (2009) 9(10): 2798-2808
Proteomic Analysis of Methylarginine-Containing Proteins in HeLa Cells by Two-Dimensional Gel Electrophoresis and Immunoblotting with a Methylarginine-Specific Antibody
Hung CJ, Lee YJ, Chen DH, Li C.
Protein J Early Edition: published 14-Apr-2009
Actin and RIG-I/MAVS signaling components translocate to mitochondria upon influenza A virus infection of human primary macrophages
Ohman T, Rintahaka J, Kalkkinen N, Matikainen S, Nyman TA.
J Immunol (2009) 182(9): 5682-92
Evolution of Nacre: Biochemistry and Proteomics of the Shell Organic Matrix of the Cephalopod Nautilus macromphalus
Marie B, Marin F, Marie A, Bédouet L, Dubost L, Alcaraz G, Milet C, Luquet G.
Chembiochem (2009) 10(9): 1495-1506
From Secretome Analysis to Immunology: CHITOSAN INDUCES MAJOR ALTERATIONS IN THE ACTIVATION OF DENDRITIC CELLS VIA A TLR4-DEPENDENT MECHANISM
Christian Villiers, Mireille Chevallet, Helene Diemer, Rachel Couderc, Heidi Freitas, Alain Van Dorsselaer, Patrice N. Marche, and Thierry Rabilloud
Mol Cell Proteomics (2009) 8(6): 1252-1264
Proteomic study via a non-gel based approach of meningococcal outer membrane vesicle vaccine obtained from strain CU385: A road map for discovery new antigens
Gil J, Betancourt LH, Sardiñas G, Yero D, Niebla O, Delgado M, GarcÃa D, Pajón R, Sánchez A, González LJ, Padrón G, Campa C, Sotolongo F, Barberá R, Guillén G, Herrera L, Besada V.
Hum Vaccin Early Edition: published 8-May-2009
Proteomic profiling of the stem cell response to retinoic acid and synthetic retinoid analogues: identification of major retinoid-inducible proteins
Maltman DJ, Christie VB, Collings JC, Barnard JH, Fenyk S, Marder TB, Whiting A, Przyborski SA.
Mol Biosyst (2009) 5(5): 458-71
Proteomics analysis of BHK-21 cells infected with a fixed strain of rabies virus
Fatemeh Zandi, Naser Eslami, Masoomeh Soheili, Ahmad Fayaz, Alireza Gholami, Behrouz Vaziri
PROTEOMICS (2009) 9(9): 2399-2407
Proteomic analysis reveals presence of platelet microparticles in endothelial progenitor cell cultures
Prokopi M, Pula G, Mayr U, Devue C, Gallagher J, Xiao Q, Boulanger CM, Westwood N, Urbich C, Willeit J, Steiner M, Breuss J, Xu Q, Kiechl S, Mayr M.
Blood Early Edition: published 15-Apr-2009
The Relevance of Carbon Dioxide Metabolism in Streptococcus thermophilus
Arioli S, Roncada P, Salzano AM, Deriu F, Corona S, Guglielmetti S, Bonizzi L, Scaloni A, Mora D.
Microbiology (2009) 155(Pt 6): 1953-65
Proteome analysis of adipocyte lipid rafts reveals that gC1qR plays essential roles in adipogenesis and insulin signal transduction
Ki-Bum Kim, Bong-Woo Kim, Hyo-Jung Choo, Young-Chan Kwon, Byung-Yoon Ahn, Jong-Soon Choi, Jae-Seon Lee, Young-Gyu Ko
PROTEOMICS (2009) 9(9): 2373-2382
Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis
Raman B, Pan C, Hurst GB, Rodriguez M Jr, McKeown CK, Lankford PK, Samatova NF, Mielenz JR.
PLoS ONE (2009) 4(4): e5271
Acclimatory responses of the Daphnia pulex proteome to environmental changes. I. Chronic exposure to hypoxia affects the oxygen transport system and carbohydrate metabolism
Zeis B, Lamkemeyer T, Paul RJ, Nunes F, Schwerin S, Koch M, Schuetz W, Madlung J, Fladerer C, Pirow R.
BMC Physiol (2009) 9(1): 7
Proteomic studies in zebrafish liver cells exposed to the brominated flame retardants HBCD and TBBPA
Kling P, Förlin L.
Ecotoxicol Environ Saf Early Edition: published 22-May-2009
A proteomic-based approach for the identification of immunodominant Cryptococcus neoformans proteins
Mattie Young, Sandra Macias, Derek Thomas, Floyd L. Wormley Jr.
PROTEOMICS (2009) 9(9): 2578-2588
Comparative proteomic and regulatory network analyses of the elongating pig conceptus
Séverine A. Degrelle, Le Ann Blomberg, Wesley M. Garrett, Robert W. Li, Neil C. Talbot
PROTEOMICS (2009) 9(10): 2678-2694
An attempt to understand kidney's protein handling function by comparing plasma and urine proteomes
Jia L, Zhang L, Shao C, Song E, Sun W, Li M, Gao Y.
PLoS ONE (2009) 4(4): e5146
New and novel markers for prostate cancer detection
Risk MC, Lin DW.
Curr Urol Rep (2009) 10(3): 179-86
Proteomics: Addressing the challenges of osteoarthritis
De Ceuninck F, Berenbaum F.
Drug Discov Today Early Edition: published 25-May-2009
Mitochondrial proteomics on human fibroblasts for identification of metabolic imbalance and cellular stress
Palmfeldt J, Vang S, Stenbroen V, Pedersen CB, Christensen JH, Bross P, Gregersen N.
Proteome Science (2009) 7(1): 20
Excretory/Secretory Proteome of the Adult Developmental Stage of Human Blood Fluke, Schistosoma japonicum
Feng Liu, Shu-Jian Cui, Wei Hu, Zheng Feng, Zhi-Qin Wang, and Ze-Guang Han
Mol Cell Proteomics (2009) 8(6): 1236-1251
Salivary biomarkers for the detection of malignant tumors that are remote from the oral cavity
Bigler LR, Streckfus CF, Dubinsky WP.
Clin Lab Med (2009) 29(1): 71-85
Molecular network of the comprehensive multiple sclerosis brain-lesion proteome
Satoh J, Tabunoki H, Yamamura T.
Mult Scler (2009) 15(5): 531-41
Identification of a membrane proteomic signature for human embryonic stem cells independent of culture conditions
Harkness L, Christiansen H, Nehlin J, Barington T, Andersen JS, Kassem M.
Stem Cell Res (2008) 1(3): 219-27
Application of SELDI-TOF-MS to identify serum biomarkers for renal cell carcinoma
Xu G, Xiang CQ, Lu Y, Kang XN, Liao P, Ding Q, Zhang YF.
Cancer Lett Early Edition: published 10-Apr-2009
Serum proteomic biomarker discovery reflective of stage and obesity in breast cancer patients
Schaub NP, Jones KJ, Nyalwidhe JO, Cazares LH, Karbassi ID, Semmes OJ, Feliberti EC, Perry RR, Drake RR.
J Am Coll Surg (2009) 208(5): 970-8
GlycoFibroTest Is a Highly Performant Liver Fibrosis Biomarker Derived from DNA Sequencer-based Serum Protein Glycomics
Dieter Vanderschaeghe, Wouter Laroy, Erwin Sablon, Philippe Halfon, Annelies Van Hecke, Joris Delanghe, and Nico Callewaert
Mol Cell Proteomics (2009) 8(5): 986-994
Tissue proteomics: a new investigative tool for renal biopsy analysis
Sedor JR.
Kidney Int (2009) 75(9): 876-9
The minor salivary gland proteome in Sjögren's syndrome
Hjelmervik TO, Jonsson R, Bolstad AI.
Oral Dis Early Edition: published 2-Apr-2009
Plasma biomarkers for Mild Cognitive Impairment and Alzheimer's disease
Song F, Poljak A, Smythe GA, Sachdev P.
Brain Res Rev Early Edition: published 20-May-2009
Discovering New Bioactive Neuropeptides in the Striatum Secretome Using in Vivo Microdialysis and Versatile Proteomics
Benoit Bernay, Marie-Claude Gaillard, Vilem Guryca, Anouk Emadali, Lauriane Kuhn, Anne Bertrand, Isabelle Detraz, Carole Carcenac, Marc Savasta, Emmanuel Brouillet, Jerome Garin, and Jean-Marc Elalouf
Mol Cell Proteomics (2009) 8(5): 946-958
Pancreas-specific Pten deficiency causes partial resistance to diabetes and elevated hepatic AKT signaling
Tong Z, Fan Y, Zhang W, Xu J, Cheng J, Ding M, Deng H.
Cell Res (2009) 19(6): 710-9
Autoimmune liver disease
Czaja AJ.
Curr Opin Gastroenterol (2009) 25(3): 215-22
Plasma proteomic analysis of patients with squamous cell carcinoma of the uterine cervix
Jeong DH, Kim HK, Prince AE, Lee DS, Kim YN, Han J, Kim KT.
J Gynecol Oncol (2008) 19(3): 173-80
Activation of the GH/IGF-1 axis by CJC-1295, a long-acting GHRH analog, results in serum protein profile changes in normal adult subjects
Sackmann-Sala L, Ding J, Frohman LA, Kopchick JJ.
Growth Horm IGF Res Early Edition: published 20-Apr-2009
Cardiovascular proteomics: implications for clinical applications
Schoenhoff FS, Fu Q, Van Eyk JE.
Clin Lab Med (2009) 29(1): 87-99
Proteomic identification of HNE-bound proteins in early Alzheimer disease: Insights into the role of lipid peroxidation in the progression of AD
Reed TT, Pierce WM, Markesbery WR, Butterfield DA.
Brain Res Early Edition: published 14-Apr-2009
Identification of a Putative Protein Profile Associated with Tamoxifen Therapy Resistance in Breast Cancer
Arzu Umar, Hyuk Kang, Annemieke M. Timmermans, Maxime P. Look, Marion E. Meijer-van Gelder, Michael A. den Bakker, Navdeep Jaitly, John W. M. Martens, Theo M. Luider, John A. Foekens, and Ljiljana Pasa-Tolic
Mol Cell Proteomics (2009) 8(6): 1278-1294
Developing Multiplexed Assays for Troponin I and Interleukin-33 in Plasma by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry
Kuhn E, Addona T, Keshishian H, Burgess M, Mani DR, Lee RT, Sabatine MS, Gerszten RE, Carr SA.
Clin Chem (2009) 55(6): 1108-17
Identification of Proteomic Differences between Squamous Cell Carcinoma of the Lung and Bronchial Epithelium
Gereon Poschmann, Barbara Sitek, Bence Sipos, Anna Ulrich, Sebastian Wiese, Christian Stephan, Bettina Warscheid, Gunter Kloppel, Ann Vander Borght, Frans C. S. Ramaekers, Helmut E. Meyer, and Kai Stuhler
Mol Cell Proteomics (2009) 8(5): 1105-1116
Proteome serological determination of tumor-associated antigens in melanoma
Forgber M, Trefzer U, Sterry W, Walden P.
PLoS ONE (2009) 4(4): e5199
Proteomics and diabetic retinopathy
Merchant ML, Klein JB.
Clin Lab Med (2009) 29(1): 139-49
Serum proteomics using mass spectrometry
Hood BL, Malehorn DE, Conrads TP, Bigbee WL.
Methods Mol Biol (2009) 520: 107-28
Identification of Proteins with Increased Expression in Rheumatoid Arthritis Synovial Tissues
Chang X, Cui Y, Zong M, Zhao Y, Yan X, Chen Y, Han J.
J Rheumatol (2009) 36(5): 872-80
Clinical proteomic applications of formalin-fixed paraffin-embedded tissues
Blonder J, Veenstra TD.
Clin Lab Med (2009) 29(1): 101-13
Identification of Early Intestinal Neoplasia Protein Biomarkers Using Laser Capture Microdissection and MALDI MS
Baogang J. Xu, Jiaqing Li, R. Daniel Beauchamp, Yu Shyr, Ming Li, M. Kay Washington, Timothy J. Yeatman, Robert H. Whitehead, Robert J. Coffey, and Richard M. Caprioli
Mol Cell Proteomics (2009) 8(5): 936-945
MALDI-TOF MS combined with magnetic beads for detecting serum protein biomarkers and establishment of boosting decision tree model for diagnosis of systemic lupus erythematosus
Huang Z, Shi Y, Cai B, Wang L, Wu Y, Ying B, Qin L, Hu C, Li Y.
Rheumatology (Oxford) (2009) 48(6): 626-31
Safety Assessment of Biotechnology Products for Potential Risk of Food Allergy: Implications of New Research
Selgrade MK, Bowman CC, Ladics GS, Privalle L, Laessig SA.
Toxicol Sci Early Edition: published 10-Apr-2009
Striatal Alterations of Secretogranin-1, Somatostatin, Prodynorphin, and Cholecystokinin Peptides in an Experimental Mouse Model of Parkinson Disease
Anna Nilsson, Maria Falth, Xiaoqun Zhang, Kim Kultima, Karl Skold, Per Svenningsson, and Per E. Andren
Mol Cell Proteomics (2009) 8(5): 1094-1104
Predictive value of combined amniotic fluid proteomic biomarkers and interleukin-6 in preterm labor with intact membranes
Cobo T, Palacio M, Navarro-Sastre A, Ribes A, Bosch J, Filella X, Gratacós E.
Am J Obstet Gynecol (2009) 200(5): 499.e1-6
Autoantibody profiling for cancer detection
Qiu J, Hanash S.
Clin Lab Med (2009) 29(1): 31-46
Changes in the Spinal Cord Proteome of an Amyotrophic Lateral Sclerosis Murine Model Determined by Differential In-gel Electrophoresis
Daniel Bergemalm, Karin Forsberg, P. Andreas Jonsson, Karin S. Graffmo, Thomas Brannstrom, Peter M. Andersen, Henrik Antti, and Stefan L. Marklund
Mol Cell Proteomics (2009) 8(6): 1306-1317
Quantitative proteomics of nasal mucus in chronic sinusitis with nasal polyposis
Al Badaai Y, Difalco MR, Tewfik MA, Samaha M.
J Otolaryngol Head Neck Surg (2009) 38(3): 381-9
Right ventricular hypertrophy with early dysfunction: A proteomics study in a neonatal model
Sheikh AM, Barrett C, Villamizar N, Alzate O, Valente AM, Herlong JR, Craig D, Lodge A, Lawson J, Milano C, Jaggers J.
J Thorac Cardiovasc Surg (2009) 137(5): 1146-53
A Tumor-Protective Role for Human Kallikrein-Related Peptidase 6 in Breast Cancer Mediated by Inhibition of Epithelial-to-Mesenchymal Transition
Pampalakis G, Prosnikli E, Agalioti T, Vlahou A, Zoumpourlis V, Sotiropoulou G.
Cancer Res (2009) 69(9): 3779-87
Global screening of human cord blood proteomes for biomarkers of toxic exposure and effect
Colquhoun DR, Goldman LR, Cole RN, Gucek M, Mansharamani M, Witter FR, Apelberg BJ, Halden RU.
Environ Health Perspect (2009) 117(5): 832-8
Proteomics of acute coronary syndromes
Didangelos A, Simper D, Monaco C, Mayr M.
Curr Atheroscler Rep (2009) 11(3): 188-95
Proteomics in Autoimmune Thyroid Eye Disease
Okrojek R, Grus FH, Matheis N, Kahaly GJ.
Horm Metab Res (2009) 41(6): 465-70
Pediatric cardiopulmonary bypass circuits: a review of studies conducted at the Penn State Pediatric Cardiac Research Laboratories
Miller A, Lu CK, Wang S, Umstead TM, Freeman WM, Vrana K, Yang S, Myers JL, Phelps DS, Zahn JD, Undar A.
J Extra Corpor Technol (2009) 41(1): P50-8
Proteomics makes progress in cartilage and arthritis research
Wilson R, Whitelock JM, Bateman JF.
Matrix Biol (2009) 28(3): 121-8
Assessing Susceptibility to Age-related Macular Degeneration with Proteomic and Genomic Biomarkers
Jiayin Gu, Gayle J. T. Pauer, Xiuzhen Yue, Umadevi Narendra, Gwen M. Sturgill, James Bena, Xiaorong Gu, Neal S. Peachey, Robert G. Salomon, Stephanie A. Hagstrom, John W. Crabb, and Clinical Genomic and Proteomic AMD Study Group
Mol Cell Proteomics (2009) 8(6): 1338-1349
Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated with Pancreatic Cancer
Fiedler GM, Leichtle AB, Kase J, Baumann S, Ceglarek U, Felix K, Conrad T, Witzigmann H, Weimann A, Schütte C, Hauss J, Büchler M, Thiery J.
Clin Cancer Res (2009) 15(11): 3812-9
Development of high-throughput mass spectrometry-based approaches for cancer biomarker discovery and implementation
Hood BL, Stewart NA, Conrads TP.
Clin Lab Med (2009) 29(1): 115-38
Innovations, challenges and future prospects of oncoproteomics
Jain KK.
Mol Oncol (2008) 2(2): 153-60
HA-tagging of putative flagellar proteins in Chlamydomonas reinhardtii identifies a novel protein of intraflagellar transport complex B
Lechtreck KF, Luro S, Awata J, Witman GB.
Cell Motil Cytoskeleton Early Edition: published 20-Apr-2009
Differential proteomic analysis of cyclosporine A-induced toxicity in renal proximal tubule cells
Puigmulé M, López-Hellin J, Suñé G, Tornavaca O, Camaño S, Tejedor A, Meseguer A.
Nephrol Dial Transplant Early Edition: published 15-Apr-2009
Identification of tumor-associated antigens as diagnostic and predictive biomarkers in cancer
Zhang JY, Looi KS, Tan EM.
Methods Mol Biol (2009) 520: 1-10
Metastasis-related Plasma Membrane Proteins of Human Breast Cancer Cells Identified by Comparative Quantitative Mass Spectrometry
Rikke Leth-Larsen, Rikke Lund, Helle V. Hansen, Anne-Vibeke Laenkholm, David Tarin, Ole N. Jensen, and Henrik J. Ditzel
Mol Cell Proteomics (2009) 8(6): 1436-1449
Microalbuminuria in type 1 diabetes mellitus is associated with enhanced excretion of the endocytic, multiligand receptors megalin and cubilin
Thrailkill KM, Nimmo T, Bunn RC, Cockrell GE, Moreau CS, Mackintosh S, Edmondson RD, Fowlkes JL.
Diabetes Care Early Edition: published 14-Apr-2009
Reverse-phase protein microarrays for theranostics and patient tailored therapy
Espina V, Liotta LA, Petricoin EF 3rd.
Methods Mol Biol (2009) 520: 89-105
Hypothermic Preservation Up-Regulates Calpain Expression and Increases Ubiquitination in Cultured Vascular Endothelial Cells: Influence of Dopamine Pretreatment
Rudic B, Song H, Breedijk A, Brinkkoetter P, Beck G, Yard B, Ponelies N.
J Surg Res Early Edition: published 19-Jan-2009
Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens
Fan AC, Deb-Basu D, Orban MW, Gotlib JR, Natkunam Y, O'Neill R, Padua RA, Xu L, Taketa D, Shirer AE, Beer S, Yee AX, Voehringer DW, Felsher DW.
Nat Med (2009) 15(5): 566-71
Serum proteomic profiling and haptoglobin polymorphisms in patients with GVHD after allogeneic hematopoietic cell transplantation
McGuirk J, Hao G, Hou W, Abhyankar S, Williams C, Yan W, Yuan J, Guan X, Belt R, Dejarnette S, Wieman J, Yan Y.
J Hematol Oncol (2009) 2(1): 17
Grade-dependent Proteomics Characterization of Kidney Cancer
Bertrand Perroud, Tatz Ishimaru, Alexander D. Borowsky, and Robert H. Weiss
Mol Cell Proteomics (2009) 8(5): 971-985
Clinical Quantitation of Prostate-specific Antigen Biomarker in the Low Nanogram/Milliliter Range by Conventional Bore Liquid Chromatography-Tandem Mass Spectrometry (Multiple Reaction Monitoring) Coupling and Correlation with ELISA Tests
Tanguy Fortin, Arnaud Salvador, Jean Philippe Charrier, Cristof Lenz, Xavier Lacoux, Aymeric Morla, Genevieve Choquet-Kastylevsky, and Jerome Lemoine
Mol Cell Proteomics (2009) 8(5): 1006-1015
Studies of keratins in tongue coating samples of hepatitis B patients by mass spectrometry
Fang Fang, Ping Liu, Haoyang Wang, Li Zhang, Jing Zhang, Yuping Gao, Liming Zeng, Yinlong Guo
Rapid Communications in Mass Spectrometry (2009) 23(11): 1703-1709
2DE for Proteome Analysis of Human Metaphase Chromosomes
Fukui K, Uchiyama S.
Methods Mol Biol (2009) 519: 259-271
A proteomic approach links decreased pyruvate kinase M2 expression to oxaliplatin resistance in patients with colorectal cancer and in human cell lines
Martinez-Balibrea E, Plasencia C, Ginés A, Martinez-Cardús A, Musulén E, Aguilera R, Manzano JL, Neamati N, Abad A.
Mol Cancer Ther (2009) 8(4): 771-8
Non-invasive biomarkers for monitoring the fibrogenic process in liver: a short survey
Gressner AM, Gao CF, Gressner OA.
World J Gastroenterol (2009) 15(20): 2433-40
Identification of a subset of breast carcinomas characterized by expression of cytokeratin 15: relationship between CK15+ progenitor/amplified cells and pre-malignant lesions and invasive disease
Celis JE, Gromova I, Cabezón T, Gromov P, Shen T, Timmermans-Wielenga V, Rank F, Moreira JM.
Mol Oncol (2007) 1(3): 321-49
Exosomal Secretion of Cytoplasmic Prostate Cancer Xenograft-derived Proteins
Flip H. Jansen, Jeroen Krijgsveld, Angelique van Rijswijk, Gert-Jan van den Bemd, Mirella S. van den Berg, Wytske M. van Weerden, Rob Willemsen, Lennard J. Dekker, Theo M. Luider, and Guido Jenster
Mol Cell Proteomics (2009) 8(6): 1192-1205
Targeted proteomic strategy for clinical biomarker discovery
Schiess R, Wollscheid B, Aebersold R.
Mol Oncol (2009) 3(1): 33-44
Proteomics and Pathway Analysis Identifies JNK Signaling as Critical for High Linear Energy Transfer Radiation-induced Apoptosis in Non-small Lung Cancer Cells
Sara Stahl, Eva Fung, Christopher Adams, Johan Lengqvist, Birgitta Mork, Bo Stenerlow, Rolf Lewensohn, Janne Lehtio, Roman Zubarev, and Kristina Viktorsson
Mol Cell Proteomics (2009) 8(5): 1117-1129
Age-related Changes in the Spatial Distribution of Human Lens {alpha}-Crystallin Products by MALDI Imaging Mass Spectrometry
Grey AC, Schey KL.
Invest Ophthalmol Vis Sci Early Edition: published 22-Apr-2009
Comprehensive proteomic analysis of human cervical-vaginal fluid using colposcopy samples
Zegels G, Van Raemdonck GA, Coen EP, Tjalma WA, Van Ostade XW.
Proteome Science (2009) 7(1): 17
Analysis of macrophage migration inhibitory factor (MIF) in patients with idiopathic pulmonary fibrosis
Bargagli E, Olivieri C, Nikiforakis N, Cintorino M, Magi B, Perari MG, Vagaggini C, Spina D, Prasse A, Rottoli P.
Respir Physiol Neurobiol Early Edition: published 20-May-2009
Comparative proteome analysis of human adenocarcinoma
Xiao G, Lu Q, Li C, Wang W, Chen Y, Xiao Z.
Med Oncol Early Edition: published 21-Apr-2009
Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma
Old WM, Shabb JB, Houel S, Wang H, Couts KL, Yen CY, Litman ES, Croy CH, Meyer-Arendt K, Miranda JG, Brown RA, Witze ES, Schweppe RE, Resing KA, Ahn NG.
Mol Cell (2009) 34(1): 115-31
CSF proteome analysis in clinically isolated syndrome (CIS): candidate markers for conversion to definite multiple sclerosis
Tumani H, Lehmensiek V, Rau D, Guttmann I, Tauscher G, Mogel H, Palm C, Hirt V, Suessmuth SD, Sapunova-Meier I, Ludolph AC, Brettschneider J.
Neurosci Lett (2009) 452(2): 214-7
Analytical considerations for mass spectrometry profiling in serum biomarker discovery
Whiteley GR, Colantonio S, Sacconi A, Saul RG.
Clin Lab Med (2009) 29(1): 57-69
Metastasis-related Plasma Membrane Proteins of Human Breast Cancer Cells Identified by Comparative Quantitative Mass Spectrometry
Rikke Leth-Larsen, Rikke Lund, Helle V. Hansen, Anne-Vibeke Laenkholm, David Tarin, Ole N. Jensen, and Henrik J. Ditzel
Mol Cell Proteomics (2009) 8(6): 1436-1449
Biochemical and proteomic effects in Procambarus clarkii after chlorpyrifos or carbaryl exposure under sublethal conditions
Vioque-Fernández A, de Almeida EA, López-Barea J.
Biomarkers Early Edition: published 1-Jun-2009
Differential Permeabilization Effects of Ca2+ and Valinomycin on the Inner and Outer Mitochondrial Membranes as Revealed by Proteomics Analysis of Proteins Released from Mitochondria
Akiko Yamada, Takenori Yamamoto, Naoshi Yamazaki, Kikuji Yamashita, Masatoshi Kataoka, Toshihiko Nagata, Hiroshi Terada, and Yasuo Shinohara
Mol Cell Proteomics (2009) 8(6): 1265-1277
Functional and Complementary Phosphorylation State Attributes of Human Insulin-like Growth Factor-Binding Protein-1 (IGFBP-1) Isoforms Resolved by Free Flow Electrophoresis
Mikkel Nissum, Majida Abu Shehab, Ute Sukop, Javad M. Khosravi, Robert Wildgruber, Christoph Eckerskorn, Victor K. M. Han, and Madhulika B. Gupta
Mol Cell Proteomics (2009) 8(6): 1424-1435
Proteomic analysis of the development and germination of date palm (Phoenix dactylifera L.) zygotic embryos
Besma Sghaier-Hammami, Luis Valledor, Noureddine Drira, Jesús V. Jorrin-Novo
PROTEOMICS (2009) 9(9): 2543-2554
DSA affinity glycoproteome of human liver tissue
Sun Q, Kang X, Zhang Y, Zhou H, Dai Z, Lu W, Zhou X, Liu X, Yang P, Liu Y.
Arch Biochem Biophys (2009) 484(1): 24-9
Proteomic analysis of the phytopathogenic fungus Botrytis cinerea during cellulose degradation
Francisco Javier Fernández-Acero, Thomas Colby, Anne Harzen, Jesús Manuel Cantoral, Jürgen Schmidt
PROTEOMICS (2009) 9(10): 2892-2902
Analysis of macrophage migration inhibitory factor (MIF) in patients with idiopathic pulmonary fibrosis
Bargagli E, Olivieri C, Nikiforakis N, Cintorino M, Magi B, Perari MG, Vagaggini C, Spina D, Prasse A, Rottoli P.
Respir Physiol Neurobiol Early Edition: published 20-May-2009
Identification of major royal jelly proteins in the brain of the honeybee Apis mellifera
Peixoto LG, Calábria LK, Garcia L, Capparelli FE, Goulart LR, Sousa MV, Espindola FS.
J Insect Physiol Early Edition: published 19-May-2009
Protein identification and mRNA analysis of phytochrome-regulated genes in Arabidopsis under red light
Li X, Yang Y, Li Y, Wang J, Xiao X, Guo X, Tang D, Liu X.
Sci China C Life Sci (2009) 52(4): 371-80
Proteomic and selected metabolite analysis of grape berry tissues under well-watered and water-deficit stress conditions
Jérôme Grimplet, Matthew D. Wheatley, Hatem Ben Jouira, Laurent G. Deluc, Grant R. Cramer, John C. Cushman
PROTEOMICS (2009) 9(9): 2503-2528
Assessing Susceptibility to Age-related Macular Degeneration with Proteomic and Genomic Biomarkers
Jiayin Gu, Gayle J. T. Pauer, Xiuzhen Yue, Umadevi Narendra, Gwen M. Sturgill, James Bena, Xiaorong Gu, Neal S. Peachey, Robert G. Salomon, Stephanie A. Hagstrom, John W. Crabb, and Clinical Genomic and Proteomic AMD Study Group
Mol Cell Proteomics (2009) 8(6): 1338-1349
Proteomic Comparison of Entamoeba histolytica and Entamoeba dispar and the Role of E. histolytica Alcohol Dehydrogenase 3 in Virulence
Davis PH, Chen M, Zhang X, Clark CG, Townsend RR, Stanley SL.
PLoS Negl Trop Dis (2009) 3(4): e415
From Secretome Analysis to Immunology: CHITOSAN INDUCES MAJOR ALTERATIONS IN THE ACTIVATION OF DENDRITIC CELLS VIA A TLR4-DEPENDENT MECHANISM
Christian Villiers, Mireille Chevallet, Helene Diemer, Rachel Couderc, Heidi Freitas, Alain Van Dorsselaer, Patrice N. Marche, and Thierry Rabilloud
Mol Cell Proteomics (2009) 8(6): 1252-1264
Distinct contractile and cytoskeletal protein patterns in the Antarctic midge are elicited by desiccation and rehydration
Aiqing Li, Joshua B. Benoit, Giancarlo Lopez-Martinez, Michael A. Elnitsky, Richard E. Lee Jr, David L. Denlinger
PROTEOMICS (2009) 9(10): 2788-2798
Identification of a membrane proteomic signature for human embryonic stem cells independent of culture conditions
Harkness L, Christiansen H, Nehlin J, Barington T, Andersen JS, Kassem M.
Stem Cell Res (2008) 1(3): 219-27
Adrenaline and reactive oxygen species elicit proteome and energetic metabolism modifications in freshly isolated rat cardiomyocytes
Costa VM, Silva R, Tavares LC, Vitorino R, Amado F, Carvalho F, Bastos Mde L, Carvalho M, Carvalho RA, Remião F.
Toxicology (2009) 260(1-3): 84-96
Proteomic analysis of hybrid poplar xylem sap
Dafoe NJ, Constabel CP.
Phytochemistry Early Edition: published 23-May-2009
Effects of Typical (Haloperidol) and Atypical (Risperidone) Antipsychotic Agents on Protein Expression in Rat Neural Stem Cells
Kashem MA, Ummehany R, Ukai W, Hashimoto E, Saito T, McGregor IS, Matsumoto I.
Neurochem Int Early Edition: published 19-May-2009
Proteome mapping of the Drosophila melanogaster male reproductive system
Nobuaki Takemori, Masa-Toshi Yamamoto
PROTEOMICS (2009) 9(9): 2484-2493
Proteome of plant peroxisomes: new perspectives on the role of these organelles in cell biology
José M. Palma, Francisco J. Corpas, Luis A. del Río
PROTEOMICS (2009) 9(9): 2301-2312
Identification of New p53 Acetylation Sites in COS-1 Cells
Anita Joubel, Robert J. Chalkley, Katalin F. Medzihradszky, Hubert Hondermarck, and Alma L. Burlingame
Mol Cell Proteomics (2009) 8(6): 1167-1173
Changes in the Spinal Cord Proteome of an Amyotrophic Lateral Sclerosis Murine Model Determined by Differential In-gel Electrophoresis
Daniel Bergemalm, Karin Forsberg, P. Andreas Jonsson, Karin S. Graffmo, Thomas Brannstrom, Peter M. Andersen, Henrik Antti, and Stefan L. Marklund
Mol Cell Proteomics (2009) 8(6): 1306-1317
The Thioredoxin-like Protein Rod-derived Cone Viability Factor (RdCVFL) Interacts with TAU and Inhibits Its Phosphorylation in the Retina
Ram Fridlich, Francois Delalande, Celine Jaillard, Jun Lu, Laetitia Poidevin, Therese Cronin, Ludivine Perrocheau, Geraldine Millet-Puel, Marie-Laure Niepon, Olivier Poch, Arne Holmgren, Alain Van Dorsselaer, Jose-Alain Sahel, and Thierry Leveillard
Mol Cell Proteomics (2009) 8(6): 1206-1218
Molecular network of the comprehensive multiple sclerosis brain-lesion proteome
Satoh J, Tabunoki H, Yamamura T.
Mult Scler (2009) 15(5): 531-41
Mitochondrial proteomics on human fibroblasts for identification of metabolic imbalance and cellular stress
Palmfeldt J, Vang S, Stenbroen V, Pedersen CB, Christensen JH, Bross P, Gregersen N.
Proteome Science (2009) 7(1): 20
Liquid chromatography/atmospheric pressure chemical ionization ion trap mass spectrometry of bilobalide in plasma and brain of rats after oral administration of its phospholipidic complex
Rossi R, Basilico F, Rossoni G, Riva A, Morazzoni P, Mauri PL.
J Pharm Biomed Anal (2009) 50(2): 224-7
Protein Extraction of Formalin-fixed Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry
Scicchitano MS, Dalmas DA, Boyce RW, Thomas HC, Frazier KS.
J Histochem Cytochem Early Edition: published 26-May-2009
The cell wall and secretory proteome of a tobacco cell line synthesising secondary wall
David J. Millar, Julian P. Whitelegge, Laurence V. Bindschedler, Catherine Rayon, Alain-Michel Boudet, Michel Rossignol, Gisèle Borderies, G. Paul Bolwell
PROTEOMICS (2009) 9(9): 2355-2372
Identification of elicitor-responsive proteins in rice leaves by a proteomic approach
Ming Liao, Yunfeng Li, Zhenzhong Wang
PROTEOMICS (2009) 9(10): 2809-2819
Chromatographic and electrophoretic resolution of proteins and protein complexes from the larval midgut microvilli of Manduca sexta
Pauchet Y, Muck A, Svatoš A, Heckel DG.
Insect Biochem Mol Biol Early Edition: published 21-May-2009
Proteomics Analysis of Epithelial Cells Reprogrammed in Cell-free Extract
Emma Pewsey, Christine Bruce, A. Stephen Georgiou, Mark Jones, Duncan Baker, Saw Yen Ow, Phillip C. Wright, Christel K. Freberg, Philippe Collas,
Mol Cell Proteomics (2009) 8(6): 1401-1412
The secreted salivary proteome of the pea aphid Acyrthosiphon pisum characterised by mass spectrometry
James C. Carolan, Carol I. J. Fitzroy, Peter D. Ashton, Angela E. Douglas, Thomas L. Wilkinson
PROTEOMICS (2009) 9(9): 2457-2467
Comprehensive proteomic analysis of human cervical-vaginal fluid using colposcopy samples
Zegels G, Van Raemdonck GA, Coen EP, Tjalma WA, Van Ostade XW.
Proteome Science (2009) 7(1): 17
The Organelle Proteome of the DT40 Lymphocyte Cell Line
Stephanie L. Hall, Svenja Hester, Julian L. Griffin, Kathryn S. Lilley, and Antony P. Jackson
Mol Cell Proteomics (2009) 8(6): 1295-1305
Identification of the Major Proteins Produced by Cultured Germline Stem Cell in Chicken
Han BK, Jung JG, Nam J, Moon JK, Kim JN, Lee SI, Kim JK, Kim H, Han JY.
J Androl Early Edition: published 28-May-2009
Proteomics-Based Identification of Anchorless Cell Wall Proteins as Vaccine Candidates against Staphylococcus aureus
Glowalla E, Tosetti B, Krönke M, Krut O.
Infect Immun Early Edition: published 13-Apr-2009
Fitness of Escherichia coli during Urinary Tract Infection Requires Gluconeogenesis and the TCA Cycle
Alteri CJ, Smith SN, Mobley HL.
PLoS Pathog (2009) 5(5): e1000448
Identification of Bacillus anthracis Spore Component Antigens Conserved across Diverse Bacillus cereus sensu lato Strains
Sanghamitra Mukhopadhyay, Arya Akmal, Andrew C. Stewart, Ru-ching Hsia, and Timothy D. Read
Mol Cell Proteomics (2009) 8(6): 1174-1191
Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas JS666
Jennings LK, Chartrand MM, Lacrampe-Couloume G, Lollar BS, Spain JC, Gossett JM.
Appl Environ Microbiol (2009) 75(11): 3733-44
Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti
de Groot A, Dulermo R, Ortet P, Blanchard L, Guérin P, Fernandez B, Vacherie B, Dossat C, Jolivet E, Siguier P, Chandler M, Barakat M, Dedieu A, Barbe V, Heulin T, Sommer S, Achouak W, Armengaud J.
PLoS Genet (2009) 5(3): e1000434
Proteomic analysis of the adaptive response of Salmonella enterica serovar Typhimurium to growth under anaerobic conditions
Encheva V, Shah HN, Gharbia SE.
Microbiology Early Edition: published 23-Apr-2009
Analysis of Bacterial Proteins by 2DE
Cash P, Argo E.
Methods Mol Biol (2009) 519: 131-44
Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis
Pannekoek Y, Huis In 't Veld R, Hopman CT, Langerak AA, Speijer D, van der Ende A.
FEMS Microbiol Lett (2009) 294(2): 216-24
Differential protein expression in Corbicula fluminea upon exposure to a Microcystis aeruginosa toxic strain
Martins JC, Leão PN, Vasconcelos V.
Toxicon Early Edition: published 13-Jan-2009
Characterization of the role of the Escherichia coli periplasmic chaperone SurA using differential proteomics
Didier Vertommen, Natividad Ruiz, Pauline Leverrier, Thomas J. Silhavy, Jean-François Collet
PROTEOMICS (2009) 9(9): 2432-2443
Novel Activities of Glycolytic Enzymes in Bacillus subtilis: INTERACTIONS WITH ESSENTIAL PROTEINS INVOLVED IN mRNA PROCESSING
Fabian M. Commichau, Fabian M. Rothe, Christina Herzberg, Eva Wagner, Daniel Hellwig, Martin Lehnik-Habrink, Elke Hammer, Uwe Volker, and Jorg
Mol Cell Proteomics (2009) 8(6): 1350-1360
Identification and characterization of a strain-dependent cystathionine beta/gamma-lyase in Lactobacillus casei potentially involved in cysteine biosynthesis
Irmler S, Schäfer H, Beisert B, Rauhut D, Berthoud H.
FEMS Microbiol Lett (2009) 295(1): 67-76
Analysis of the Actinobacillus pleuropneumoniae HlyX (FNR) regulon and identification of iron-regulated protein B as an essential virulence factor
Falk F. R. Buettner, Ibrahim M. Bendalla, Janine T. Bossé, Jochen Meens, John H. E. Nash, Elisabeth Härtig, Paul R. Langford, Gerald-F. Gerlach
PROTEOMICS (2009) 9(9): 2383-2398
The high-affinity phosphate transporter Pst in Proteus mirabilis HI4320 and its importance in biofilm formation
O'May GA, Jacobsen SM, Longwell M, Stoodley P, Mobley HL, Shirtliff ME.
Microbiology (2009) 155(Pt 5): 1523-35
iTRAQ quantitative analysis of Francisella tularensis ssp. holarctica live vaccine strain and Francisella tularensis ssp. tularensis SCHU S4 response to different temperatures and stationary phases of growth
Juraj Lenco, Marek Link, Vojtech Tambor, Jitka Zaková, Lukas Cerveny, and Jiri Stulik
PROTEOMICS (2009) 9(10): 2875-2882
Global screening of human cord blood proteomes for biomarkers of toxic exposure and effect
Colquhoun DR, Goldman LR, Cole RN, Gucek M, Mansharamani M, Witter FR, Apelberg BJ, Halden RU.
Environ Health Perspect (2009) 117(5): 832-8
Protein Profiles in Zebrafish (Danio rerio) Embryos Exposed to PFOS
Shi X, Yeung LW, Lam PK, Wu RS, Zhou B.
Toxicol Sci Early Edition: published 27-May-2009
Safety Assessment of Biotechnology Products for Potential Risk of Food Allergy: Implications of New Research
Selgrade MK, Bowman CC, Ladics GS, Privalle L, Laessig SA.
Toxicol Sci Early Edition: published 10-Apr-2009
Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment
Kohji Nagano, Takashi Shinkawa, Hironori Mutoh, Osamu Kondoh, Sayuri Morimoto, Noriyuki Inomata, Motooki Ashihara, Nobuya Ishii, Yuko Aoki, Masayuki Haramura
PROTEOMICS (2009) 9(10): 2861-2874
Variable slope normalization of reverse phase protein arrays
E. Shannon Neeley, Steven M. Kornblau, Kevin R. Coombes, and Keith A. Baggerly
Bioinformatics (2009) 25(11): 1384-1389
Semiconductor quantum dots for multiplexed bio-detection on solid-state microarrays
Rousserie G, Sukhanova A, Even-Desrumeaux K, Fleury F, Chames P, Baty D, Oleinikov V, Pluot M, Cohen JH, Nabiev I.
Crit Rev Oncol Hematol Early Edition: published 19-May-2009
Application of laser microdissection and reverse-phase protein microarrays to the molecular profiling of cancer signal pathway networks in the tissue microenvironment
Espina V, Wulfkuhle J, Liotta LA.
Clin Lab Med (2009) 29(1): 1-13
The relative influence of phosphorylation and methylation on responsiveness of peptides to MALDI and ESI mass spectrometry
Jan Gropengiesser, Balamurugan T. Varadarajan, Heike Stephanowitz, Eberhard Krause
Journal of Mass Spectrometry (2009) 44(5): 821-831
Studying the effects of correlation on protein selection in proteomics data
Savita Venkataramani, Dayanand N. Naik
PROTEOMICS (2009) 9(10): 2883-2887
Protein-protein interaction studies on protein arrays: Effect of detection strategies on signal to background ratios
Hurst R, Hook B, Slater M, Hartnett J, Storts DR, Nath N.
Anal Biochem Early Edition: published 21-May-2009
Estimating accuracy of RNA-Seq and microarrays with proteomics
Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P.
BMC Genomics (2009) 10(1): 161
Peptide microarrays for determination of cross-reactivity
Thiele A.
Methods Mol Biol (2009) 524: 225-34
Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis
Sarah L. Keasey, Kara E. Schmid, Michael S. Lee, James Meegan, Patricio Tomas, Michael Minto, Alexander P. Tikhonov, Barry Schweitzer, and Robert G. Ulrich
Mol Cell Proteomics (2009) 8(5): 924-935
Developing Multiplexed Assays for Troponin I and Interleukin-33 in Plasma by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry
Kuhn E, Addona T, Keshishian H, Burgess M, Mani DR, Lee RT, Sabatine MS, Gerszten RE, Carr SA.
Clin Chem (2009) 55(6): 1108-17
Novel Proteomics Strategy Brings Insight into the Prevalence of SUMO-2 Target Sites
Henri A. Blomster, Ville Hietakangas, Jianmin Wu, Petri Kouvonen, Sampsa Hautaniemi, and Lea Sistonen
Mol Cell Proteomics (2009) 8(6): 1382-1390
Oxidative Stress-Induced Posttranslational Modification of Proteins as a Target of Functional Food
Naito Y, Yoshikawa T.
Forum Nutr (2009) 61: 39-54
The Thioredoxin-like Protein Rod-derived Cone Viability Factor (RdCVFL) Interacts with TAU and Inhibits Its Phosphorylation in the Retina
Ram Fridlich, Francois Delalande, Celine Jaillard, Jun Lu, Laetitia Poidevin, Therese Cronin, Ludivine Perrocheau, Geraldine Millet-Puel, Marie-Laure Niepon, Olivier Poch, Arne Holmgren, Alain Van Dorsselaer, Jose-Alain Sahel, and Thierry Leveillard
Mol Cell Proteomics (2009) 8(6): 1206-1218
A Strategy for Precise and Large Scale Identification of Core Fucosylated Glycoproteins
Wei Jia, Zhuang Lu, Yan Fu, Hai-Peng Wang, Le-Heng Wang, Hao Chi, Zuo-Fei Yuan, Zhao-Bin Zheng, Li-Na Song, Huan-Huan Han, Yi-Min Liang, Jing-Lan Wang, Yun Cai, Yu-Kui Zhang, Yu-Lin Deng, Wan-Tao Ying, Si-Min He, and Xiao-Hong Qian
Mol Cell Proteomics (2009) 8(5): 913-923
Therapeutically targeting protein-glycan interactions
Rek A, Krenn E, Kungl A.
Br J Pharmacol Early Edition: published 9-Apr-2009
Direct selection of monoclonal phosphospecific antibodies without prior phosphoamino acid mapping
Vielemeyer O, Yuan H, Moutel S, Saint-Fort R, Tang D, Nizak C, Goud B, Wang Y, Perez F.
J Biol Chem Early Edition: published 27-May-2009
Negative ion fragmentations of deprotonated peptides containing post-translational modifications: diphosphorylated systems containing Ser, Thr and Tyr. A characteristic phosphate/phosphate cyclisation. A joint experimental and theoretical study
Hayley J. Andreazza, Tianfang Wang, Daniel Bilusich, Peter Hoffmann, John H. Bowie
Rapid Communications in Mass Spectrometry (2009) 23(12): 1825-1833
MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields
Xuefeng Xia, Song Zhang, Yu Su, and Zhirong Sun
Bioinformatics (2009) 25(11): 1433-1434
Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment
Kohji Nagano, Takashi Shinkawa, Hironori Mutoh, Osamu Kondoh, Sayuri Morimoto, Noriyuki Inomata, Motooki Ashihara, Nobuya Ishii, Yuko Aoki, Masayuki Haramura
PROTEOMICS (2009) 9(10): 2861-2874
Functional and Complementary Phosphorylation State Attributes of Human Insulin-like Growth Factor-Binding Protein-1 (IGFBP-1) Isoforms Resolved by Free Flow Electrophoresis
Mikkel Nissum, Majida Abu Shehab, Ute Sukop, Javad M. Khosravi, Robert Wildgruber, Christoph Eckerskorn, Victor K. M. Han, and Madhulika B. Gupta
Mol Cell Proteomics (2009) 8(6): 1424-1435
Negative ion fragmentations of deprotonated peptides containing post-translational modifications. An unusual cyclisation/rearrangement involving phosphotyrosine; a joint experimental and theoretical study
Tianfang Wang, Hayley J. Andreazza, Daniel Bilusich, John H. Bowie
Rapid Communications in Mass Spectrometry (2009) 23(11): 1669-1677
Detection of Protein Glutathionylation
Gianazza E, Eberini I, Ghezzi P.
Methods Mol Biol (2009) 519: 397-415
Typical 2-Cys peroxiredoxins - modulation by covalent transformations and noncovalent interactions
Aran M, Ferrero DS, Pagano E, Wolosiuk RA.
FEBS J (2009) 276(9): 2478-93
The proteolytic activity of insulin-degrading enzyme: a mass spectrometry study
Giuseppe Grasso, Enrico Rizzarelli, Giuseppe Spoto
Journal of Mass Spectrometry (2009) 44(5): 735-741
System-wide changes to SUMO modifications in response to heat shock
Golebiowski F, Matic I, Tatham MH, Cole C, Yin Y, Nakamura A, Cox J, Barton GJ, Mann M, Hay RT.
Sci Signal (2009) 2(72): ra24
Large Scale Localization of Protein Phosphorylation by Use of Electron Capture Dissociation Mass Spectrometry
Steve M. M. Sweet, Christopher M. Bailey, Debbie L. Cunningham, John K. Heath, and Helen J. Cooper
Mol Cell Proteomics (2009) 8(5): 904-912
Unifying Fluorescence Microscopy and Mass Spectrometry for Studying Protein Complexes in Cells
Changhui Deng, Xinghua Xiong, and Andrew N. Krutchinsky
Mol Cell Proteomics (2009) 8(6): 1413-1423
Chemical Approaches To Perturb, Profile, and Perceive Glycans
Agard NJ, Bertozzi CR.
Acc Chem Res Early Edition: published 10-Apr-2009
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Eric L. Peterson, Jane Kondev, Julie A. Theriot, and Rob Phillips
Bioinformatics (2009) 25(11): 1356-1362
Mass spectrometric characterisation and quantitation of selected low molecular mass compounds from the venom of Haplopelma lividum (Theraphosidae)
Sara Moore, W. Franklin Smyth, Victor A. Gault, Edmund O'Kane, Stephen McClean
Rapid Communications in Mass Spectrometry (2009) 23(12): 1747-1755
Peptide microarrays for profiling of modification state-specific antibodies
Zerweck J, Masch A, Schutkowski M.
Methods Mol Biol (2009) 524: 169-80
Identification of New p53 Acetylation Sites in COS-1 Cells
Anita Joubel, Robert J. Chalkley, Katalin F. Medzihradszky, Hubert Hondermarck, and Alma L. Burlingame
Mol Cell Proteomics (2009) 8(6): 1167-1173
All-liquid separations, protein microarrays, and mass spectrometry to interrogate serum proteomes: an application to serum glycoproteomics
Patwa TH, Qiu Y, Zhao J, Simeone DM, Lubman DM.
Methods Mol Biol (2009) 520: 75-87
Host cell interactome of tyrosine-phosphorylated bacterial proteins
Selbach M, Paul FE, Brandt S, Guye P, Daumke O, Backert S, Dehio C, Mann M.
Cell Host Microbe (2009) 5(4): 397-403
DSA affinity glycoproteome of human liver tissue
Sun Q, Kang X, Zhang Y, Zhou H, Dai Z, Lu W, Zhou X, Liu X, Yang P, Liu Y.
Arch Biochem Biophys (2009) 484(1): 24-9
N-glycosylation microheterogeneity and site occupancy of an Asn-X-Cys sequon in plasma-derived and recombinant protein C
Geun-Cheol Gil, William H. Velander, Kevin E. Van Cott
PROTEOMICS (2009) 9(9): 2555-2567
Structural studies on Helicobacter pylori 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase using electrospray ionization mass spectrometry: a tetrameric complex composed of dimeric dimers
Zhili Li, Apurba Kumar Sau
Rapid Communications in Mass Spectrometry (2009) 23(11): 1573-1578
Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma
Old WM, Shabb JB, Houel S, Wang H, Couts KL, Yen CY, Litman ES, Croy CH, Meyer-Arendt K, Miranda JG, Brown RA, Witze ES, Schweppe RE, Resing KA, Ahn NG.
Mol Cell (2009) 34(1): 115-31
Identification of Nitroxyl-induced Modifications in Human Platelet Proteins Using a Novel Mass Spectrometric Detection Method
Michael D. Hoffman, Geraldine M. Walsh, Jason C. Rogalski, and Juergen Kast
Mol Cell Proteomics (2009) 8(5): 887-903
In Silico Analysis of Phosphoproteome Data Suggests a Rich-get-richer Process of Phosphosite Accumulation over Evolution
Nozomu Yachie, Rintaro Saito, Junichi Sugahara, Masaru Tomita, and Yasushi Ishihama
Mol Cell Proteomics (2009) 8(5): 1061-1071
Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry
Hin-Koon Woo, Eden P. Go, Linh Hoang, Sunia A. Trauger, Benjamin Bowen, Gary Siuzdak, Trent R. Northen
Rapid Communications in Mass Spectrometry (2009) 23(12): 1849-1855
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species
Ayshwarya Ravichandran, Naoyuki Sugiyama, Masaru Tomita, Sanjay Swarup, Yasushi Ishihama
PROTEOMICS (2009) 9(10): 2764-2775
Targeted proteomic strategy for clinical biomarker discovery
Schiess R, Wollscheid B, Aebersold R.
Mol Oncol (2009) 3(1): 33-44
Glycoproteomic analysis by two-dimensional electrophoresis
Comunale MA, Mehta A.
Methods Mol Biol (2009) 520: 59-74
De novo sequence analysis and intact mass measurements for characterization of phycocyanin subunit isoforms from the blue-green alga Aphanizomenon flos-aquae
Sara Rinalducci, Peter Roepstorff, Lello Zolla
Journal of Mass Spectrometry (2009) 44(4): 503-515
RNF2 is the target for phosphorylation by the p38 MAPK and ERK signaling pathways
Prema S. Rao, Arun Satelli, Sheng Zhang, Sanjay K. Srivastava, Kalkunte S. Srivenugopal, U. Subrahmanyeswara Rao
PROTEOMICS (2009) 9(10): 2776-2787
Mice Deficient in Ribosomal Protein S6 Phosphorylation Suffer from Muscle Weakness that Reflects a Growth Defect and Energy Deficit
Ruvinsky I, Katz M, Dreazen A, Gielchinsky Y, Saada A, Freedman N, Mishani E, Zimmerman G, Kasir J, Meyuhas O.
PLoS ONE (2009) 4(5): e5618
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin, David M. Kristensen, and Olivier Lichtarge
Bioinformatics (2009) 25(11): 1426-1427
Protein sumoylation sites prediction based on two-stage feature selection
Lu L, Shi XH, Li SJ, Xie ZQ, Feng YL, Lu WC, Li YX, Li H, Cai YD.
Mol Divers Early Edition: published 27-May-2009
Detection and structural features of the ?B2-B3-crystallin heterodimer by radical probe mass spectrometry (RP-MS)
Hélène Diemer, Cédric Atmanene, Sarah Sanglier, Bethny Morrissey, Alain Van Dorsselaer, Kevin M. Downard
Journal of Mass Spectrometry (2009) 44(5): 803-812
Charting the molecular network of the drug target Bcr-Abl
Brehme M, Hantschel O, Colinge J, Kaupe I, Planyavsky M, Köcher T, Mechtler K, Bennett KL, Superti-Furga G.
Proc Natl Acad Sci U S A (2009) 106(18): 7414-9
Therapeutically targeting protein-glycan interactions
Rek A, Krenn E, Kungl A.
Br J Pharmacol Early Edition: published 9-Apr-2009
High-throughput T-cell epitope discovery through MHC Peptide exchange
Hadrup SR, Toebes M, Rodenko B, Bakker AH, Egan DA, Ovaa H, Schumacher TN.
Methods Mol Biol (2009) 524: 383-405
Unbiased proteomic screen for binding proteins to modified lysines on histone H3
Doug W. Chan, Yi Wang, Meng Wu, Jiemin Wong, Jun Qin, Yingming Zhao
PROTEOMICS (2009) 9(9): 2343-2354
Two-dimensional native electrophoretic analysis of respiratory supercomplexes from Yarrowia lipolytica
Esther Nübel, Ilka Wittig, Stefan Kerscher, Ulrich Brandt, Hermann Schägger
PROTEOMICS (2009) 9(9): 2408-2418
Drosophila proteins interacting with metallothioneins: A metal-dependent recognition
Laura Tio, Maria-Ayelén Pagani, Sílvia Atrian
PROTEOMICS (2009) 9(9): 2568-2577
Host cell interactome of tyrosine-phosphorylated bacterial proteins
Selbach M, Paul FE, Brandt S, Guye P, Daumke O, Backert S, Dehio C, Mann M.
Cell Host Microbe (2009) 5(4): 397-403
New dimensions in the study of protein complexes using quantitative mass spectrometry
Oeljeklaus S, Meyer HE, Warscheid B.
FEBS Lett (2009) 583(11): 1674-83
Identification and characterization of proteins interacting with SIRT1 and SIRT3: implications in the anti-aging and metabolic effects of sirtuins
Ivy K. M. Law, Ling Liu, Aimin Xu, Karen S. L. Lam, Paul M. Vanhoutte, Chi-Ming Che, Priscilla T. Y. Leung, Yu Wang
PROTEOMICS (2009) 9(9): 2444-2456
Use of Site-Specific Protein-DNA Photocrosslinking of Purified Complexes to Analyze the Topology of the RNA Polymerase II Transcription Initiation Complex
Forget D, Domecq C, Coulombe B.
Methods Mol Biol (2009) 543: 439-51
Synthesis of biotin-tagged chemical cross-linkers and their applications for mass spectrometry
Sebyung Kang, Liyuan Mou, Jason Lanman, Sadanandan Velu, Wayne J. Brouillette, Peter E. Prevelige Jr.
Rapid Communications in Mass Spectrometry (2009) 23(11): 1719-1726
The utility of functional interaction and cluster analysis in CNS proteomics
Deighton RF, Short DM, McGregor RJ, Gow AJ, Whittle IR, McCulloch J.
J Neurosci Methods (2009) 180(2): 321-9
Protein-protein interaction studies on protein arrays: Effect of detection strategies on signal to background ratios
Hurst R, Hook B, Slater M, Hartnett J, Storts DR, Nath N.
Anal Biochem Early Edition: published 21-May-2009
Inferring protein-protein interactions from multiple protein domain combinations
Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA.
Methods Mol Biol (2009) 541: 1-17
A Complex-based Reconstruction of the Saccharomyces cerevisiae Interactome
Haidong Wang, Boyko Kakaradov, Sean R. Collins, Lena Karotki, Dorothea Fiedler, Michael Shales, Kevan M. Shokat, Tobias C. Walther, Nevan J. Krogan, and Daphne Koller
Mol Cell Proteomics (2009) 8(6): 1361-1381
Mass spectrometry-based absolute quantification of microsomal cytochrome P450 2D6 in human liver
Elmar Langenfeld, Ulrich M. Zanger, Klaus Jung, Helmut E. Meyer, Katrin Marcus
PROTEOMICS (2009) 9(9): 2313-2323
Quantitative proteomics of nasal mucus in chronic sinusitis with nasal polyposis
Al Badaai Y, Difalco MR, Tewfik MA, Samaha M.
J Otolaryngol Head Neck Surg (2009) 38(3): 381-9
StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry
Bas van Breukelen, Henk W. P. van den Toorn, Madalina M. Drugan, and Albert J. R. Heck
Bioinformatics (2009) 25(11): 1472-1473
Statistical Model to Analyze Quantitative Proteomics Data Obtained by 18O/16O Labeling and Linear Ion Trap Mass Spectrometry: Application to the Study of Vascular Endothelial Growth Factor-induced Angiogenesis in Endothelial Cells
Inmaculada Jorge, Pedro Navarro, Pablo Martinez-Acedo, Estefania Nunez, Horacio Serrano, Arantzazu Alfranca, Juan Miguel Redondo, and Jesus Vazquez
Mol Cell Proteomics (2009) 8(5): 1130-1149
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Quantitative Comparison of the Membrane Proteomes of Self-renewing and Differentiating Human Embryonic Stem Cells
Tatyana A. Prokhorova, Kristoffer T. G. Rigbolt, Pia T. Johansen, Jeanette Henningsen, Irina Kratchmarova, Moustapha Kassem, and Blagoy Blagoev
Mol Cell Proteomics (2009) 8(5): 959-970
Protein profile in hepatitis B virus replicating rat primary hepatocytes and HepG2 cells by iTRAQ-coupled 2-D LC-MS/MS analysis: Insights on liver angiogenesis
Jianhua Zhang, Dandan Niu, Jianjun Sui, Chi Bun Ching, Wei Ning Chen
PROTEOMICS (2009) 9(10): 2836-2845
SISCAPA Peptide Enrichment on Magnetic Beads Using an In-line Bead Trap Device
N. Leigh Anderson, Angela Jackson, Derek Smith, Darryl Hardie, Christoph Borchers, and Terry W. Pearson
Mol Cell Proteomics (2009) 8(5): 995-1005
iTRAQ quantitative analysis of Francisella tularensis ssp. holarctica live vaccine strain and Francisella tularensis ssp. tularensis SCHU S4 response to different temperatures and stationary phases of growth
Juraj Lenco, Marek Link, Vojtech Tambor, Jitka Zaková, Lukas Cerveny, and Jiri Stulik
PROTEOMICS (2009) 9(10): 2875-2882