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SPS' DigestIssue 49, 11-Mar-2008 |
Computational Methods and Algorithms for Mass-Spectrometry Based Differential Proteomics
Mavroudi, Seferina; Papadimitriou, Stergios; Kossida, Sophia; Likothanassis, Spyridon D.; Vlahou, Antonia
Current Proteomics (2007) 4(4): 223-234
Organizing a competition on clinical mass spectrometry based proteomic diagnosis
Mertens B
Stat Appl Genet Mol Biol (2008) 7: Article3
Statistical data processing in clinical proteomics
Smit S, Hoefsloot HC, Smilde AK.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 4-Nov-2007
Pfam: a domain-centric method for analyzing proteins and proteomes
Mistry J, Finn R.
Methods Mol Biol (2007) 396: 43-58
Autocorrelated logistic ridge regression for prediction based on proteomics spectra
Goeman JJ
Stat Appl Genet Mol Biol (2008) 7: Article10
PRIDE: new developments and new datasets
Jones P, Cote RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H
Nucl Acids Res (2008) 36(Database issue): D878-83
Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data
Meuleman W, Engwegen JY, Gast MC, Beijnen JH, Reinders MJ, Wessels LF.
BMC Bioinformatics (2008) 9(1): 88
A classification model for the leiden proteomics competition
Hoefsloot HC, Smit S, Smilde AK
Stat Appl Genet Mol Biol (2008) 7: Article8
Alignment of LC-MS images, with applications to biomarker discovery and protein identification
Mathias Vandenbogaert, Sébastien Li-Thiao-Té, Hans-Michael Kaltenbach, Runxuan Zhang, Tero Aittokallio, Benno Schwikowski
PROTEOMICS (2008) 8(4): 650-672
Current Status of Computational Approaches for Protein Identification Using Tandem Mass Spectra
Zhang, Xiang; Oh, Cheolhwan; Riley, Catherine P.; Buck, Charles
Current Proteomics (2007) 4(3): 121-130
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP.
Proc Natl Acad Sci U S A (2008) 105(5): 1454-9
Combinatorial approaches for mass spectra recalibration
Bocker S, Makinen V.
IEEE/ACM Trans Comput Biol Bioinform (2008) 5(1): 91-100
LOCATE: a mammalian protein subcellular localization database
Sprenger J, Lynn Fink J, Karunaratne S, Hanson K, Hamilton NA, Teasdale RD
Nucl Acids Res (2008) 36(Database issue): D230-3
An image analysis suite for spot detection and spot matching in two-dimensional electrophoresis gels
Thitiwan Srinark, Chandra Kambhamettu
ELECTROPHORESIS (2008) 29(3): 706-715
Classification of breast cancer versus normal samples from mass spectrometry profiles using linear discriminant analysis of important features selected by random forest
Datta S
Stat Appl Genet Mol Biol (2008) 7: Article7
Evolution of an Arsenal: Structural and Functional Diversification of the Venom System in the Advanced Snakes (Caenophidia)
Bryan G. Fry, Holger Scheib, Louise van der Weerd, Bruce Young, JudithMcNaughtan, S. F. Ryan Ramjan, Nicolas Vidal, Robert E. Poelmann, and Janette A. Norman
Mol Cell Proteomics (2008) 7(2): 215-246
Systematic Assessment of the Benefits and Caveats in Mining Microbial Post-Translational Modifications from Shotgun Proteomic Data: The Response of Shewanella oneidensis to Chromate Exposure
Melissa R. Thompson, Dorothea K. Thompson, and Robert L. Hettich
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 648-658
Experiment-specific estimation of Peptide identification probabilities using a randomized database
Higdon R, Hogan JM, Kolker N, van Belle G, Kolker E.
OMICS (2007) 11(4): 351-66
Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study
Marengo E, Robotti E, Bobba M, Milli A, Campostrini N, Righetti SC, Cecconi D, Righetti PG.
Anal Bioanal Chem Early Edition: published 29-Jan-2008
Precise score for the prediction of peptides cleaved by the proteasome
Ido Ginodi, Tal Vider-Shalit, Lea Tsaban, and Yoram Louzoun
Bioinformatics (2008) 24(4): 477-483
In Silico Characterization of Proteins: UniProt, InterPro and Integr8
Mulder NJ, Kersey P, Pruess M, Apweiler R.
Mol Biotechnol (2008) 38(2): 165-77
DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
Sebastian Bocker, Zsuzsanna Liptak, Marcel Martin, Anton Pervukhin, and Henner Sudek
Bioinformatics (2008) 24(4): 591-593
On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
Ye J, Liu H, Kirmiz C, Lebrilla CB, Rocke DM.
BMC Bioinformatics (2007) 8(1): 477
ConoServer, a database for conopeptide sequences and structures
Quentin Kaas, Jan-C. Westermann, Reena Halai, Conan K. L. Wang, and David J. Craik
Bioinformatics (2008) 24(3): 445-446
Developing a discrimination rule between breast cancer patients and controls using proteomics mass spectrometric data: a three-step approach
Heidema AG, Nagelkerke N
Stat Appl Genet Mol Biol (2008) 7: Article5
Bioinformatic Requirements for Protein Database Searching Using Predicted Epitopes from Disease-associated Antibodies
Gerassimos Bastas, Seshi R. Sompuram, Brian Pierce, Kodela Vani, and Steven A. Bogen
Mol Cell Proteomics (2008) 7(2): 247-256
Support vector machine approach to separate control and breast cancer serum samples
Pham TV, van de Wiel MA, Jimenez CR
Stat Appl Genet Mol Biol (2008) 7: Article11
PARPs Database: A LIMS systems for protein-protein interaction data mining or Laboratory Information management system
Droit A, Hunter JM, Rouleau M, Ethier C, Picard-Cloutier A, Bourgais D, Poirier GG.
BMC Bioinformatics (2007) 8(1): 483
Glycomics: towards bioinformatic approaches to understanding glycosylation
Mahal LK.
Anticancer Agents Med Chem (2008) 8(1): 37-51
InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison
Mulder N, Apweiler R.
Methods Mol Biol (2007) 396: 59-70
Computational prediction of protein-protein interactions
Skrabanek L, Saini HK, Bader GD, Enright AJ.
Mol Biotechnol (2008) 38(1): 1-17
Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data
Jeffrey S. Morris, Brittan N. Clark, and Howard B. Gutstein
Bioinformatics (2008) 24(4): 529-536
Application of the random forest classification method to peaks detected from mass spectrometric proteomic profiles of cancer patients and controls
Barrett JH, Cairns DA
Stat Appl Genet Mol Biol (2008) 7: Article4
PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains
Gong W, Zhou D, Ren Y, Wang Y, Zuo Z, Shen Y, Xiao F, Zhu Q, Hong A, Zhou X, Gao X, Li T
Nucl Acids Res (2008) 36(Database issue): D679-83
CIFTER: Automated Charge-State Determination for Peptide Tandem Mass Spectra
Seungjin Na, Eunok Paek, and Cheolju Lee
ANALYTICAL CHEMISTRY (2008) 80(5): 1520-1528
Characterization of Proteomic and Metabolomic Responses to Dietary Factors and Supplements
Astle J, Ferguson JT, German JB, Harrigan GG, Kelleher NL, Kodadek T, Parks BA, Roth MJ, Singletary KW, Wenger CD, Mahady GB.
J Nutr (2007) 137(12): 2787-2793
Are protein complexes made of cores, modules and attachments?
Chi Nam Ignatius Pang, James Robert Krycer, Angela Lek, Marc Ronald Wilkins
PROTEOMICS (2008) 8(3): 425-434
Comparative proteomics and correlated signaling network of rat hippocampus in the pilocarpine model of temporal lobe epilepsy
Xin-Yu Liu, Jin-Liang Yang, Li-Juan Chen, Ying Zhang, Ming-Li Yang, Yong-Yang Wu, Fu-Qiang Li, Ming-Hai Tang, Shu-Fang Liang, Yu-Quan Wei
PROTEOMICS (2008) 8(3): 582-603
Proteomic Studies on Plant-Pathogen Interaction in Compatible and Incompatible Systems
Butt, Yoki K.w.o.k-C.h.u.; Lo, Samuel C.h.u.n-L.a.p.
Current Proteomics (2007) 4(3): 141-156
A mass spectrometry-based strategy for detecting and characterizing endogenous proteinase activities in complex biological samples
Sarah Robinson, Richard K. Niles, H. Ewa Witkowska, Kirsten J. Rittenbach, Robert J. Nichols, Jonathan A. Sargent, Scott E. Dixon, Akraporn Prakobphol, Steven C. Hall, Susan J. Fisher, Markus Hardt
PROTEOMICS (2008) 8(3): 435-445
Platelet Factor-4 Is an Indicator of Blood Count Recovery in Acute Myeloid Leukemia Patients in Complete Remission
Jin Young Kim, Ho-Jun Song, Hoi-Jeong Lim, Myung-Geun Shin, Jae Seong Kim, Hyeoung-Joon Kim, Baik Yoon Kim, and Seung-won Lee
Mol Cell Proteomics (2008) 7(2): 431-441
2DE identification of proteins exhibiting turnover and phosphorylation dynamics during sea urchin egg activation
Roux MM, Radeke MJ, Goel M, Mushegian A, Foltz KR.
Dev Biol (2008) 313(2): 630-47
Comparative proteomic analysis of livers from ketotic cows
Xu C, Wang Z.
Vet Res Commun (2008) 32(3): 263-273
Proteomic investigation of the aggregation phenomenon in Lactobacillus crispatus
Siciliano RA, Cacace G, Mazzeo MF, Morelli L, Elli M, Rossi M, Malorni A.
Biochim Biophys Acta (2008) 1784(2): 335-42
Differential expression of glycosomal and mitochondrial proteins in the two major life-cycle stages of Trypanosoma brucei
Vertommen D, Van Roy J, Szikora JP, Rider MH, Michels PA, Opperdoes FR.
Mol Biochem Parasitol (2008) 158(2): 189-201
Hsp60 regulation of tumor cell apoptosis
Ghosh JC, Dohi T, Kang BH, Altieri DC.
J Biol Chem (2008) 283(8): 5188-94
Proteomics profiling of hepatic mitochondria in heterozygous Sod2+/- mice, an animal model of discreet mitochondrial oxidative stress
Yie Hou Lee, Urs A. Boelsterli, Qingsong Lin, Maxey C. M. Chung
PROTEOMICS (2008) 8(3): 555-568
MicroRNA-target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis
Tian Z, Greene AS, Pietrusz JL, Matus IR, Liang M.
Genome Res (2008) 18(3): 404-11
Soybean Proteomics
Komatsu, Setsuko; Toorchi, Mahmoud; Yukawa, Kiyoshi
Current Proteomics (2007) 4(3): 182-186
Characterization of the Human Skeletal Muscle Proteome by One-dimensional Gel Electrophoresis and HPLC-ESI-MS/MS
Kurt Hojlund, Zhengping Yi, Hyonson Hwang, Benjamin Bowen, Natalie Lefort, Charles R. Flynn, Paul Langlais, Susan T. Weintraub, and Lawrence J. Mandarino
Mol Cell Proteomics (2008) 7(2): 257-267
Proteomic analysis of the pH response in the fungal pathogen Candida glabrata
Pia Schmidt, Janet Walker, Laura Selway, David Stead, Zhikang Yin, Brice Enjalbert, Michael Weig, Alistair J. P. Brown
PROTEOMICS (2008) 8(3): 534-544
Proteomic analysis of hydroxyapatite interaction proteins in bone
Zhou HY.
Ann N Y Acad Sci (2007) 1116: 323-6.
The histone chaperone protein Nucleosome Assembly Protein-1 (hNAP-1) binds HIV-1 Tat and promotes viral transcription
Vardabasso C, Manganaro L, Lusic M, Marcello A, Giacca M.
Retrovirology (2008) 5(1): 8
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome
Buza TJ, McCarthy FM, Burgess SC.
BMC Genomics (2007) 8(1): 425
Highly Efficient Classification and Identification of Human Pathogenic Bacteria by MALDI-TOF MS
Sen-Yung Hsieh, Chiao-Li Tseng, Yun-Shien Lee, An-Jing Kuo, Chien-FengSun, Yen-Hsiu Lin, and Jen-Kun Chen
Mol Cell Proteomics (2008) 7(2): 448-456
Intracellular complexes of the 2 subunit of the nicotinic acetylcholine receptor in brain identified by proteomics
Kabbani N, Woll MP, Levenson R, Lindstrom JM, Changeux JP.
Proc Natl Acad Sci U S A (2007) 104(51): 20570-5
Proteomic identification of ZO-1/2 as a novel scaffold for Src/Csk regulatory circuit
Saito K, Enya K, Oneyama C, Hikita T, Okada M.
Biochem Biophys Res Commun (2008) 366(4): 969-75
Proteomic analysis of augmented immune responses in mouse by prime-and-boost immunization strategy with DNA vaccine coding HBsAg and rHBsAg protein
Wang Y, Li DA, He Y, Wang F, Guo YJ, Yang F, Zhou Q, Sun SH.
Vaccine (2007) 25(48): 8146-53
Identification of host proteins associated to retroviral vector particles by proteomic analysis of highly purified vector preparations
Segura MM, Garnier A, Di Falco MR, Whissell G, Meneses-Acosta A, Arcand N, Kamen A.
J Virol (2008) 82(3): 1107-17
Proteomic analysis of human osteoarthritic chondrocytes reveals protein changes in stress and glycolysis
Cristina Ruiz-Romero, Vanessa Carreira, Ignacio Rego, Silvia Remeseiro, María J. López-Armada, Francisco J. Blanco
PROTEOMICS (2008) 8(3): 495-507
Proteomic analysis of Saccharomyces cerevisiae
Trong Khoa Pham, Phillip C Wright
Expert Review of Proteomics (2007) 4(6): 793-813
Monitoring Mouse Prostate Development by Profiling and Imaging Mass Spectrometry
Pierre Chaurand, Mohammad A. Rahman, Tamela Hunt, James A. Mobley, Guangyu Gu, Joey C. Latham, Richard M. Caprioli, and Susan Kasper
Mol Cell Proteomics (2008) 7(2): 411-423
PRAS40 and PRR5-Like Protein Are New mTOR Interactors that Regulate Apoptosis
Thedieck K, Polak P, Kim ML, Molle KD, Cohen A, Jenö P, Arrieumerlou C, Hall MN.
PLoS ONE (2007) 2(11): e1217
Differential expression of cardiac mitochondrial proteins
Julia R. Smith, Isaac R. Matus, Daniel A. Beard, Andrew S. Greene
PROTEOMICS (2008) 8(3): 446-462
Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin
Zamora DO, Riviere M, Choi D, Pan Y, Planck SR, Rosenbaum JT, David LL, Smith JR.
Mol Vis (2007) 13: 2058-65.
The Phb1/2 phospho-complex is required for mitochondrial homeostasis and survival of human T cells
Ross JA, Nagy ZS, Kirken RA.
J Biol Chem (2008) 283(8): 4699-713
Proteomic analysis of human thyroid fine needle aspiration fluid
Giusti L, Iacconi P, Ciregia F, Giannaccini G, Basolo F, Donatini G, Miccoli P, Lucacchini A.
J Endocrinol Invest (2007) 30(10): 865-9
Association of Mortalin (HSPA9) with Liver Cancer Metastasis and Prediction for Early Tumor Recurrence
Xin Yi, John M. Luk, Nikki P. Lee, Jirun Peng, Xisheng Leng, Xin-Yuan Guan, George K. Lau, Laura Beretta, and Sheung-Tat Fan
Mol Cell Proteomics (2008) 7(2): 315-325
Application of Proteomics in the Discovery of Candidate Protein Biomarkers in a Diabetes Autoantibody Standardization Program Sample Subset
Thomas O. Metz, Wei-Jun Qian, Jon M. Jacobs, Marina A. Gritsenko, Ronald J. Moore, Ashoka D. Polpitiya, Matthew E. Monroe, David G. Camp II, Patricia W. Mueller, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 698-707
Serological Immunoreactivity against Colon Cancer Proteome Varies upon Disease Progression
Lucia De Monte, Francesca Sanvito, Stefano Olivieri, Fiammetta Viganò, Claudio Doglioni, Matteo Frasson, Marco Braga, Angela Bachi, Paolo Dellabona, Maria Pia Protti, and Massimo Alessio
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 504-514
SELDI-TOF MS Whole Serum Proteomic Profiling with IMAC Surface Does Not Reliably Detect Prostate Cancer
McLerran D, Grizzle WE, Feng Z, Thompson IM, Bigbee WL, Cazares LH, Chan DW, Dahlgren J, Diaz J, Kagan J, Lin D, Malik G, Oelschlager D, Partin A, Randolph T, Sokoll L, Srivastava S, Srivastava S, Thornquist M, Troyer D, Wright GL, Zhang Z, Zhu L, Semmes OJ.
Clin Chem (2008) 54(1): 53-60
Mitochondrial Dysfunction, Oxidative Stress, and Apoptosis Revealed by Proteomic and Transcriptomic Analyses of the Striata in Two Mouse Models of Parkinson’s Disease
Mark H. Chin, Wei-Jun Qian, Haixing Wang, Vladislav A. Petyuk, Joshua S. Bloom, Daniel M. Sforza, Goran Laćan, Dahai Liu, Arshad H. Khan, Rita M. Cantor, Diana J. Bigelow, William P. Melega, David G. Camp II, Richard D. Smith, and Desmond J. Smith
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 666-677
Systematic high-content proteomic analysis reveals substantial immunologic changes in colorectal cancer
Berndt U, Philipsen L, Bartsch S, Wiedenmann B, Baumgart DC, Hämmerle M, Sturm A.
Cancer Res (2008) 68(3): 880-8
Differential proteome of bone marrow mesenchymal stem cells from osteoarthritis patients
RollÃn R, Marco F, Camafeita E, Calvo E, López-Durán L, Jover JA, López JA, Fernández-Gutiérrez B.
Osteoarthritis Cartilage Early Edition: published 25-Jan-2008
Plasma and Serum Levels of Tissue Inhibitor of Metalloproteinases-1 Are Associated with Prognosis in Node-negative Breast Cancer: A Prospective Study
Sidse Ornbjerg Wurtz, Susanne Moller, Henning Mouridsen, Pernille Briaemer Hertel, Esbern Friis, and Nils Brunner
Mol Cell Proteomics (2008) 7(2): 424-430
Proteomics in leptospirosis research: towards molecular diagnostics and vaccine development
Thongboonkerd V.
Expert Rev Mol Diagn (2008) 8(1): 53-61
Cigarette Smoke Induces an Unfolded Protein Response in the Human Lung: A Proteomic Approach
Kelsen SG, Duan X, Ji R, Perez O, Liu C, Merali S.
Am J Respir Cell Mol Biol Early Edition: published 13-Dec-2007
Proteomic approach to investigate MRSA
Francois P, Scherl A, Hochstrasser D, Schrenzel J.
Methods Mol Biol (2007) 391: 179-200
Ovarian cancer proteomics: Many technologies one goal
Kothandaraman Narasimhan, Zhao Changqing, Mahesh Choolani
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 195-218
Proteomic profiling of Rhipicephalus (Boophilus) microplus midgut responses to infection with Babesia bovis
Rachinsky A, Guerrero FD, Scoles GA.
Vet Parasitol Early Edition: published 27-Dec-2007
Identification of accessible human cancer biomarkers using ex vivo chemical proteomic strategies
Philippe Kischel, David Waltregny, Vincent Castronovo
Expert Review of Proteomics (2007) 4(6): 727-739
Evolutionary medicine: A meaningful connection between omics, disease, and treatment
Mones Abu-Asab, Mohamed Chaouchi, Hakima Amri
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 122-134
Hypoxic conditions and iron restriction affect the cell-wall proteome of Candida albicans grown under vagina-simulative conditions
Sosinska GJ, de Groot PW, Teixeira de Mattos MJ, Dekker HL, de Koster CG, Hellingwerf KJ, Klis FM.
Microbiology (2008) 154(Pt 2): 510-20
Case-control breast cancer study of MALDI-TOF proteomic mass spectrometry data on serum samples
van der Werff MP, Mertens B, de Noo ME, Bladergroen MR, Dalebout HC, Tollenaar RA, Deelder AM
Stat Appl Genet Mol Biol (2008) 7: Article2
Identification of Hepatocellular-Carcinoma-Associated Antigens and Autoantibodies by Serological Proteome Analysis Combined with Protein Microarray
Lan Li, Su-hong Chen, Chao-hui Yu, You-ming Li, and Sheng-qi Wang
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 611-620
Streptococcus pneumoniae: proteomics of surface proteins for vaccine development
Morsczeck C, Prokohova T, Sigh J, Pfeiffer M, Bille-Nielsen M, Petersen J, Boysen A, Kofoed T, Frimodt-Møller N, Nyborg-Nielsen P, Schrotz-King P.
Clin Microbiol Infect (2008) 14(1): 74-81
Biomarker discovery for kidney diseases by mass spectrometry
Niwa T.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 1-Nov-2007
Ubiquitin-proteasome system dysfunction in Parkinson's disease: current evidence and controversies
Kah-Leong Lim
Expert Review of Proteomics (2007) 4(6): 769-781
A sodium dodecyl sulfate-polyacrylamide gel electrophoresis-liquid chromatography tandem mass spectrometry analysis of bovine cartilage tissue response to mechanical compression injury and the inflammatory cytokines tumor necrosis factor alpha and interleukin-1beta
Stevens AL, Wishnok JS, Chai DH, Grodzinsky AJ, Tannenbaum SR.
Arthritis Rheum (2008) 58(2): 489-500
Mortalin: A Protein Associated With Progression of Parkinson Disease?
Shi M, Jin J, Wang Y, Beyer RP, Kitsou E, Albin RL, Gearing M, Pan C, Zhang J.
J Neuropathol Exp Neurol Early Edition: published 18-Jan-2008
Serum Proteomics and Biomarkers in Hepatocellular Carcinoma and Chronic Liver Disease
Zinkin NT, Grall F, Bhaskar K, Otu HH, Spentzos D, Kalmowitz B, Wells M, Guerrero M, Asara JM, Libermann TA, Afdhal NH.
Clin Cancer Res (2008) 14(2): 470-477
Bronchoalveolar lavage fluid proteome in bronchiolitis obliterans syndrome: possible role for surfactant protein a in disease onset
Meloni F, Salvini R, Bardoni AM, Passadore I, Solari N, Vitulo P, Oggionni T, Viganò M, Pozzi E, Fietta AM.
J Heart Lung Transplant (2007) 26(11): 1135-43
Combined metabolomic and proteomic analysis of human atrial fibrillation
Mayr M, Yusuf S, Weir G, Chung YL, Mayr U, Yin X, Ladroue C, Madhu B, Roberts N, De Souza A, Fredericks S, Stubbs M, Griffiths JR, Jahangiri M, Xu Q, Camm AJ.
J Am Coll Cardiol (2008) 51(5): 585-94
Proteomic analysis of rat brain mitochondria following exposure to dopamine quinone: Implications for Parkinson disease
Van Laar VS, Dukes AA, Cascio M, Hastings TG.
Neurobiol Dis (2008) 29(3): 477-89
Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infection
Rawson PM, Molette C, Videtta M, Altieri L, Franceschini D, Donato T, Finocchi L, Propato A, Paroli M, Meloni F, Mastroianni CM, d'Ettorre G, Sidney J, Sette A, Barnaba V.
Nat Med (2007) 13(12): 1431-9
Immunoproteomics: From biomarker discovery to diagnostic applications
Harold Tjalsma, Renée M. J. Schaeps, Dorine W. Swinkels
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 167-180
Proteomic diagnosis of Sjögren's syndrome
Laura Giusti, Chiara Baldini, Laura Bazzichi, Stefano Bombardieri, Antonio Lucacchini
Expert Review of Proteomics (2007) 4(6): 757-767
Human Heart Failure: A Proteomics Perspective
Goel, Arvind; Rakwal, Randeep; Agrawal, Ganesh K.
Current Proteomics (2007) 4(3): 174-181
Proteomic analysis of autoantibodies in neuropsychiatric systemic lupus erythematosus patient with white matter hyperintensities on brain MRI
Kimura A, Sakurai T, Tanaka Y, Hozumi I, Takahashi K, Takemura M, Saito K, Seishima M, Inuzuka T.
Lupus (2008) 17(1): 16-20
Differential proteomic analysis of nuclear matrix in muscle-invasive bladder cancer: Potential to improve diagnosis and prognosis
Barboro P, Rubagotti A, Orecchia P, Spina B, Truini M, Repaci E, Carmignani G, Romagnoli A, Introini C, Boccardo F, Carnemolla B, Balbi C.
Cell Oncol (2008) 30(1): 13-26
Proteomic approach to biomarker discovery in cancer tissue from lung adenocarcinoma among nonsmoking Chinese women in Hong Kong
Au JS, Cho WC, Yip TT, Law SC.
Cancer Invest (2008) 26(2): 128-35
Mass spectrometry analysis of gliadins in celiac disease
Ferranti P, Mamone G, Picariello G, Addeo F.
J Mass Spectrom (2007) 42(12): 1531-1548
Analysis of MALDI-TOF Mass Spectrometry Data for Discovery of Peptide and Glycan Biomarkers of Hepatocellular Carcinoma
Habtom W. Ressom, Rency S. Varghese, Lenka Goldman, Yanming An, Christopher A. Loffredo, Mohamed Abdel-Hamid, Zuzana Kyselova, Yehia Mechref, Milos Novotny, Steven K Drake, and Radoslav Goldman
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 603-610
Comprehensive proteomics analysis of autophagy-deficient mouse liver
Matsumoto N, Ezaki J, Komatsu M, Takahashi K, Mineki R, Taka H, Kikkawa M, Fujimura T, Takeda-Ezaki M, Ueno T, Tanaka K, Kominami E.
Biochem Biophys Res Commun (2008) 368(3): 643-9
Modulation of cancer cell line differentiation: A neglected proteomic analysis with potential implications in pathophysiology, diagnosis, prognosis, and therapy of cancer
Roberto Scatena, Patrizia Bottoni, Bruno Giardina
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 229-237
Proteomic characterisation of the whole secretome of Legionella pneumophila and functional analysis of outer membrane vesicles
Galka F, Wai SN, Kusch H, Engelmann S, Hecker M, Schmeck B, Hippenstiel S, Uhlin BE, Steinert M.
Infect Immun Early Edition: published 4-Feb-2008
Clinical application of proteomics approaches in vascular diseases
Xiao-Li Wang, Alex Fu, Craig Spiro, Hon-Chi Lee
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 238-250
A subcelluar proteomic investigation into vincristine-resistant gastric cancer cell line
Yang YX, Chen ZC, Zhang GY, Yi H, Xiao ZQ.
J Cell Biochem Early Edition: published 5-Feb-2008
Urinary Proteomic Biomarkers in Coronary Artery Disease
Lukas U. Zimmerli, Eric Schiffer, Petra Zurbig, David M. Good, Markus Kellmann, Laetitia Mouls, Andrew R. Pitt, Joshua J. Coon, Roland E. Schmieder, Karlheinz H. Peter, Harald Mischak, Walter Kolch, Christian Delles, and Anna F. Dominiczak
Mol Cell Proteomics (2008) 7(2): 290-298
Proteomic analysis of human thyroid fine needle aspiration fluid
Giusti L, Iacconi P, Ciregia F, Giannaccini G, Basolo F, Donatini G, Miccoli P, Lucacchini A.
J Endocrinol Invest (2007) 30(10): 865-9
Potential of urinary biomarkers in early bladder cancer diagnosis
Lam T, Nabi G.
Expert Rev Anticancer Ther (2007) 7(8): 1105-1115
Possibilities of Two-Dimensional Gel Electrophoresis in the Understanding of Human Disease
Lopez, Jose L.; Bermudez-Crespo, Jose
Current Proteomics (2007) 4(4): 187-197
Quantitative Proteomic Approaches to Investigate the Membrane Proteome in Neuropsychiatric Disorders
Chan, Man K.; Bahn, Sabine
Current Proteomics (2007) 4(3): 131-140
Proteomics and naturally occurring animal diseases: Opportunities for animal and human medicine
Mary K. Doherty, Robert J. Beynon, Phillip D. Whitfield
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 135-141
Circulating tumor cells: detection, molecular profiling and future prospects
Karine Jacob, Caroline Sollier, Nada Jabado
Expert Review of Proteomics (2007) 4(6): 741-756
Using Proteomic Analysis of the Human Amniotic Fluid to Identify Histologic Chorioamnionitis
Buhimschi IA, Zambrano E, Pettker CM, Bahtiyar MO, Paidas M, Rosenberg VA, Thung S, Salafia CM, Buhimschi CS.
Obstet Gynecol (2008) 111(2): 403-412
Identification of serum biomarkers for nasopharyngeal carcinoma by proteomic analysis
Wei YS, Zheng YH, Liang WB, Zhang JZ, Yang ZH, Lv ML, Jia J, Zhang L.
Cancer (2008) 112(3): 544-51
Proteomic analysis of human amniotic fluid from Rh(-) pregnancy
Hassan MI, Kumar V, Singh TP, Yadav S.
Prenat Diagn (2008) 28(2): 102-108
“Product Ion Monitoring” Assay for Prostate-Specific Antigen in Serum Using a Linear Ion-Trap
Vathany Kulasingam, Christopher R. Smith, Ihor Batruch, Alan Buckler, Douglas A. Jeffery, and Eleftherios P. Diamandis
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 640-647
Integration of DIGE and Bioinformatics Analyses Reveals a Role of the Antiobesity Agent Tungstate in Redox and Energy Homeostasis Pathways in Brown Adipose Tissue
Silvia Barcelo-Batllori, Susana G. Kalko, Yaiza Esteban, Silvia Moreno, Maria C. Carmona, and Ramon Gomis
Mol Cell Proteomics (2008) 7(2): 378-393
Identification of Novel Nasopharyngeal Carcinoma Biomarkers by Laser Capture Microdissection and Proteomic Analysis
Cheng AL, Huang WG, Chen ZC, Peng F, Zhang PF, Li MY, Li F, Li JL, Li C, Yi H, Yi B, Xiao ZQ.
Clin Cancer Res (2008) 14(2): 435-445
Intracellular complexes of the 2 subunit of the nicotinic acetylcholine receptor in brain identified by proteomics
Kabbani N, Woll MP, Levenson R, Lindstrom JM, Changeux JP.
Proc Natl Acad Sci U S A (2007) 104(51): 20570-5
Involvement of Mitogen-Activated Protein Kinase Signaling in Growth and Rupture of Human Intracranial Aneurysms
Laaksamo E, Tulamo R, Baumann M, Dashti R, Hernesniemi J, Juvela S, Niemelä M, Laakso A.
Stroke (2008) 39(3): 886-92
Serum proteomic patterns for ovarian cancer monitoring
Helleman J, van der Vlies D, Jansen MP, Luider TM, van der Burg ME, Stoter G, Berns EM.
Int J Gynecol Cancer Early Edition: published 19-Nov-2007
A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol
Blankman JL, Simon GM, Cravatt BF.
Chem Biol (2007) 14(12): 1347-56
Proteomics, nanotechnology and molecular diagnostics
Christopher J. Johnson, Nikolay Zhukovsky, Anthony E. G. Cass, Judit M. Nagy
PROTEOMICS (2008) 8(4): 715-730
Kinase signaling pathways as potential targets in the treatment of Parkinson's disease
Elisa Greggio, Andrew Singleton
Expert Review of Proteomics (2007) 4(6): 783-792
Comparative analysis of MRSA
Takeuchi F, Baba T, Hiramatsu K.
Methods Mol Biol (2007) 391: 153-68
Proteomics Analysis of the Causative Agent of Typhoid Fever
Charles Ansong, Hyunjin Yoon, Angela D. Norbeck, Jean K. Gustin, Jason E. McDermott, Heather M. Mottaz, Joanne Rue, Joshua N. Adkins, Fred Heffron, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 546-557
Discovery of diagnostic serum biomarkers of gastric cancer using proteomics
Katie Wing-kei Lam, Samuel Chun-lap Lo
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 219-228
Profiling the Monascus pilosus Proteome during Nitrogen Limitation
Lin WY, Chang JY, Hish CH, Pan TM.
J Agric Food Chem (2008) 56(2): 433-41
Identification and characterization of a new member of snake venom thrombin inhibitors from Bothrops insularis using a proteomic approach
Oliveira-Carvalho AL, Guimarães PR, Abreu PA, Dutra DL, Junqueira-de-Azevedo IL, Rodrigues CR, Ho PL, Castro HC, Zingali RB.
Toxicon Early Edition: published 14-Dec-2007
High-Throughput Analysis of Rat Liver Plasma Membrane Proteome by a Nonelectrophoretic In-Gel Tryptic Digestion Coupled with Mass Spectrometry Identification
Rui Cao, QuanYuan He, Jian Zhou, QuanZe He, Zhen Liu, XianChun Wang, Ping Chen, Jingyun Xie, and SongPing Liang
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 535-545
Comparative proteome analysis of differentially expressed proteins induced by Al toxicity in soybean
Zhen Y, Qi JL, Wang SS, Su J, Xu GH, Zhang MS, Miao L, Peng XX, Tian D, Yang YH.
Physiol Plant (2007) 131(4): 542-54
Proteomic analysis of the LPS-induced stress response in rat chondrocytes reveals induction of innate immune response components in articular cartilage
Haglund L, Bernier SM, Onnerfjord P, Recklies AD.
Matrix Biol (2008) 27(2): 107-18
Proteomic identification of the MYST domain histone acetyltransferase TIP60 (HTATIP) as a co-activator of the myeloid transcription factor C/EBPalpha
Bararia D, Trivedi AK, Zada AA, Greif PA, Mulaw MA, Christopeit M, Hiddemann W, Bohlander SK, Behre G.
Leukemia Early Edition: published 31-Jan-2008
Highly Robust, Automated, and Sensitive Online TiO2-Based Phosphoproteomics Applied To Study Endogenous Phosphorylation in Drosophila melanogaster
Martijn W. H. Pinkse, Shabaz Mohammed, Joost W. Gouw, Bas van Breukelen, Harmjan R. Vos, and Albert J. R. Heck
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 687-697
The Left Ventricle Proteome Differentiates Middle-Aged and Old Left Ventricles in Mice
Qiuxia Dai, G. Patricia Escobar, Kevin W. Hakala, Jessica M. Lambert, Susan T. Weintraub, and Merry L. Lindsey
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 756-765
A proteomic study reveals the diversified distribution of plasma membrane-associated proteins in rat hepatocytes
Li X, Cao J, Jin Q, Xie C, He Q, Cao R, Xiong J, Chen P, Wang X, Liang S.
J Cell Biochem Early Edition: published 4-Feb-2008
Proteomic Analysis of Calcium Alginate-Immobilized Saccharomyces cerevisiae under High-Gravity Fermentation Conditions
Trong Khoa Pham and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 515-525
Snake Venomics of Central American Pitvipers: Clues for Rationalizing the Distinct Envenomation Profiles of Atropoides nummifer and Atropoides picadoi
Yamileth Angulo, José Escolano, Bruno Lomonte, José María Gutiérrez, Libia Sanz, and Juan J. Calvete
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 708-719
Cartilage proteomics: Challenges, solutions and recent advances
Richard Wilson, John F. Bateman
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 251-263
Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts
Mastronunzio JE, Tisa LS, Normand P, Benson DR.
BMC Genomics (2008) 9(1): 47
High-resolution 2-DE for resolving proteins, protein adducts and complexes in plasma
Giovanni Candiano, Laura Santucci, Andrea Petretto, Barbara Pavone, Piero Del Boccio, Luca Musante, Maurizio Bruschi, Giorgio Federici, Rosanna Gusmano, Andrea Urbani, Gian M. Ghiggeri
ELECTROPHORESIS (2008) 29(3): 682-694
The Mammary Epithelial Cell Secretome and Its Regulation by Signal Transduction Pathways
Jon M. Jacobs, Katrina M. Waters, Loel E. Kathmann, David G. Camp, II, H. Steven Wiley, Richard D. Smith, and Brian D. Thrall
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 558-569
A proteomic study shows differential regulation of stress, redox regulation and peroxidase proteins by iron supply and the transcription factor FER
Brumbarova T, Matros A, Mock HP, Bauer P.
Plant J Early Edition: published 23-Jan-2008
Mitochondrial Dysfunction, Oxidative Stress, and Apoptosis Revealed by Proteomic and Transcriptomic Analyses of the Striata in Two Mouse Models of Parkinson’s Disease
Mark H. Chin, Wei-Jun Qian, Haixing Wang, Vladislav A. Petyuk, Joshua S. Bloom, Daniel M. Sforza, Goran Laćan, Dahai Liu, Arshad H. Khan, Rita M. Cantor, Diana J. Bigelow, William P. Melega, David G. Camp II, Richard D. Smith, and Desmond J. Smith
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 666-677
A comparative proteomic analysis of tomato leaves in response to waterlogging stress
Ahsan N, Lee DG, Lee SH, Kang KY, Bahk JD, Choi MS, Lee IJ, Renaut J, Lee BH.
Physiol Plant (2007) 131(4): 555-70
Saliva analysis by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF/MS): from sample collection to data analysis
Papale M, Pedicillo MC, Di Paolo S, Thatcher BJ, Lo Muzio L, Bufo P, Rocchetti MT, Centra M, Ranieri E, Gesualdo L.
Clin Chem Lab Med (2008) 46(1): 89-99
Glomerulus proteome analysis with two-dimensional gel electrophoresis and mass spectrometry
Tryggvason S, Nukui M, Oddsson A, Tryggvason K, Jörnvall H.
Cell Mol Life Sci (2007) 64(24): 3317-35
Proteomic Analysis of a Membrane Preparation from Rat Olfactory Sensory Cilia
Mayer U, Ungerer N, Klimmeck D, Warnken U, Schnölzer M, Frings S, Möhrlen F.
Chem Senses (2008) 33(2): 145-62
Proteomics investigation of protein expression changes in ouabain induced apoptosis in human umbilical vein endothelial cells
Qiu J, Gao HQ, Li BY, Shen L.
J Cell Biochem Early Edition: published 4-Feb-2008
Quantitative analysis of auxin-regulated proteins from basal part of leaf sheaths in rice by two-dimensional difference gel electrophoresis
Shi F, Takasaki H, Komatsu S.
Phytochemistry (2008) 69(3): 637-46
Increased levels of carbonic anhydrase II in the developing Down syndrome brain
Palminiello S, Kida E, Kaur K, Walus M, Wisniewski KE, Wierzba-Bobrowicz T, Rabe A, Albertini G, Golabek AA.
Brain Res Early Edition: published 22-Nov-2007
Phosphoproteome of Resting Human Platelets
René P. Zahedi, Urs Lewandrowski, Julia Wiesner, Stefanie Wortelkamp, Jan Moebius, Claudia Schütz, Ulrich Walter, Stepan Gambaryan, and Albert Sickmann
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 526-534
Evaluation of strategy for analyzing mouse liver plasma membrane proteome
Chen P, Zhang L, Li X, Wang X, Cao R, Liu Z, Xiong J, Peng X, Wei Y, Ying X, Wang X, Liang S.
Sci China C Life Sci (2007) 50(6): 731-8
Lessons from the stem cell proteome
Gesslbauer B, Krenn E, Zenzmaier C, Preisegger KH, Kungl AJ.
Curr Stem Cell Res Ther (2006) 1(3): 395-409
Expression and immunogenicity of six putative variable surface proteins in Mycoplasma mycoides subsp. mycoides SC
Hamsten C, Westberg J, Bölske G, Ayling R, Uhlén M, Persson A.
Microbiology (2008) 154(Pt 2): 539-49
The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression
Elias DA, Tollaksen SL, Kennedy DW, Mottaz HM, Giometti CS, McLean JS, Hill EA, Pinchuk GE, Lipton MS, Fredrickson JK, Gorby YA.
Arch Microbiol Early Edition: published 21-Nov-2007
Comparative Proteome Analysis of the Outer Membrane Proteins of in Vitro-Induced Multi-Drug Resistant Neisseria gonorrhoeae
Yoo JS, Seong WK, Kim TS, Park YK, Oh HB, Yoo CK.
Microbiol Immunol (2007) 51(12): 1171-7
Hypoxic conditions and iron restriction affect the cell-wall proteome of Candida albicans grown under vagina-simulative conditions
Sosinska GJ, de Groot PW, Teixeira de Mattos MJ, Dekker HL, de Koster CG, Hellingwerf KJ, Klis FM.
Microbiology (2008) 154(Pt 2): 510-20
Streptococcus pneumoniae: proteomics of surface proteins for vaccine development
Morsczeck C, Prokohova T, Sigh J, Pfeiffer M, Bille-Nielsen M, Petersen J, Boysen A, Kofoed T, Frimodt-Møller N, Nyborg-Nielsen P, Schrotz-King P.
Clin Microbiol Infect (2008) 14(1): 74-81
Mucosal vaccination with phage-displayed tumour antigens identified through proteomics-based strategy inhibits the growth and metastasis of 4T1 breast adenocarcinoma
Shadidi M, Sørensen D, Dybwad A, Furset G, Sioud M.
Int J Oncol (2008) 32(1): 241-7
Proteomic profiling identifies afamin as a potential biomarker for ovarian cancer
Jackson D, Craven RA, Hutson RC, Graze I, Lueth P, Tonge RP, Hartley JL, Nickson JA, Rayner SJ, Johnston C, Dieplinger B, Hubalek M, Wilkinson N, Perren TJ, Kehoe S, Hall GD, Daxenbichler G, Dieplinger H, Selby PJ, Banks RE.
Clin Cancer Res (2007) 13(24): 7370-9
Heat-Shock Response in Arabidopsis thaliana Explored by Multiplexed Quantitative Proteomics Using Differential Metabolic Labeling
Magnus Palmblad, Davinia J. Mills, and Laurence V. Bindschedler
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 780-785
A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli
Chen CS, Korobkova E, Chen H, Zhu J, Jian X, Tao SC, He C, Zhu H.
Nat Methods (2008) 5(1): 69-74
Differential expression of proteins in response to the interaction between the pathogen Fusarium graminearum and its host, Hordeum vulgare
Jennifer Geddes, François Eudes, André Laroche, L. Brent Selinger
PROTEOMICS (2008) 8(3): 545-554
Proteomic investigation of the aggregation phenomenon in Lactobacillus crispatus
Siciliano RA, Cacace G, Mazzeo MF, Morelli L, Elli M, Rossi M, Malorni A.
Biochim Biophys Acta (2008) 1784(2): 335-42
Proteomics Analysis of the Causative Agent of Typhoid Fever
Charles Ansong, Hyunjin Yoon, Angela D. Norbeck, Jean K. Gustin, Jason E. McDermott, Heather M. Mottaz, Joanne Rue, Joshua N. Adkins, Fred Heffron, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 546-557
Integrating microarray and proteomics data to predict the response on cetuximab in patients with rectal cancer
Daemen A, Gevaert O, De Bie T, Debucquoy A, Machiels JP, De Moor B, Haustermans K.
Pac Symp Biocomput (2008) 1: 166-77
Proteomic Identification of Interleukin-2 Therapy Response in Metastatic Renal Cell Cancer
Jones J, Otu HH, Grall F, Spentzos D, Can H, Aivado M, Belldegrun AS, Pantuck AJ, Libermann TA.
J Urol (2008) 179(2): 730-6
Drug resistance in cancer - searching for mechanisms, markers and therapeutic agents
O'Connor R, Clynes M, Dowling P, O'Donovan N, O'Driscoll L.
Expert Opin Drug Metab Toxicol (2007) 3(6): 805-17
Radon-induced proteomic profile of lung tissue in rats
Xu NY, Zhang SP, Nie JH, Li JX, Tong J.
J Toxicol Environ Health A (2008) 71(6): 361-6
Proteomic analysis of rat brain mitochondria following exposure to dopamine quinone: Implications for Parkinson disease
Van Laar VS, Dukes AA, Cascio M, Hastings TG.
Neurobiol Dis (2008) 29(3): 477-89
Proteomic analysis of mouse islets after multiple low-dose streptozotocin injection
Xie X, Li S, Liu S, Lu Y, Shen P, Ji J.
Biochim Biophys Acta (2008) 1784(2): 276-84
Proteomic analysis for inhibitory effect of chitosan oligosaccharides on 3T3-L1 adipocyte differentiation
Md. Atiar Rahman, Suresh G. Kumar, Sang Woo Kim, Hye Jin Hwang, Yu Mi Baek, Sung Hak Lee, Hee Sun Hwang, Yun Hee Shon, Kyung Soo Nam, Jong Won Yun
PROTEOMICS (2008) 8(3): 569-581
Venomics: unravelling the complexity of animal venoms with mass spectrometry
P. Escoubas, L. Quinton, G. M. Nicholson
Journal of Mass Spectrometry (2008) 43(3): 279-295
Estradiol in vivo regulation of brain mitochondrial proteome
Nilsen J, Irwin RW, Gallaher TK, Brinton RD.
J Neurosci (2007) 27(51): 14069-77
Quantitative Protein Network Monitoring in Response to DNA Damage
Satoshi Nishizuka, Sundhar Ramalingam, Brett Spurrier, Frank L. Washburn, Ramya Krishna, Peter Honkanen, Lynn Young, Tsutomu Shimura, Patricia S. Steeg, and John Austin
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 803-808
Unique proteomic features induced by a potential antiglioma agent, Nordy (dl-nordihydroguaiaretic acid), in glioma cells
Xiu-Wu Bian, Jian-Ping Xu, Yi-Fang Ping, Yan Wang, Jian-Hong Chen, Cheng-Ping Xu, Yu-Zhang Wu, Jun Wu, Xiang-Dong Zhou, Yi-Sheng Chen, Jing-Quan Shi, Ji Ming Wang
PROTEOMICS (2008) 8(3): 484-494
Analysis of 2,3,7,8-Tetrachlorodibenzo-p-dioxin-induced Proteome Changes in 5L Rat Hepatoma Cells Reveals Novel Targets of Dioxin Action Including the Mitochondrial Apoptosis Regulator VDAC2
Hakan Sarioglu, Stefanie Brandner, Markus Haberger, Carola Jacobsen, Josef Lichtmannegger, Mark Wormke, and Ulrich Andrae
Mol Cell Proteomics (2008) 7(2): 394-410
Gender-specific proteomic responses in zebrafish liver following exposure to a selected mixture of brominated flame retardants(,)
Kling P, Norman A, Andersson PL, Norrgren L, Förlin L.
Ecotoxicol Environ Saf Early Edition: published 5-Feb-2008
A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli
Chen CS, Korobkova E, Chen H, Zhu J, Jian X, Tao SC, He C, Zhu H.
Nat Methods (2008) 5(1): 69-74
Mass spectrometry-based proteomics of fungal wall glycoproteins
Yin QY, de Groot PW, de Koster CG, Klis FM.
Trends Microbiol (2008) 16(1): 20-6
Integral Protein Microarrays for the Identification of Lung Cancer Antigens in Sera That Induce a Humoral Immune Response
Juan Madoz-Gurpide, Rork Kuick, Hong Wang, David E. Misek, and Sam M. Hanash
Mol Cell Proteomics (2008) 7(2): 268-281
Development and use of a partial Mycobacterium avium subspecies paratuberculosis protein array
John P. Bannantine, W. Ray Waters, Judith R. Stabel, Mitchell V. Palmer, Lingling Li, Vivek Kapur, Michael L. Paustian
PROTEOMICS (2008) 8(3): 463-474
Absolute and Site-Specific Quantification of Protein Phosphorylation Using Integrated Elemental and Molecular Mass Spectrometry: Its Potential To Assess Phosphopeptide Enrichment Procedures
Ana Pereira Navaza, Jorge Ruiz Encinar, Montserrat Carrascal, Joaquín Abi n, and Alfredo Sanz-Medel
ANALYTICAL CHEMISTRY (2008) 80(5): 1777-1787
Phosphorylation site analysis of the anti-inflammatory and mRNA-destabilizing protein tristetraprolin
Heping Cao, Leesa J Deterding, Perry J Blackshear
Expert Review of Proteomics (2007) 4(6): 711-726
On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
Ye J, Liu H, Kirmiz C, Lebrilla CB, Rocke DM.
BMC Bioinformatics (2007) 8(1): 477
Neuroproteomics and the Detection of Regulatory Phosphosites
Mansuy, Isabelle M.; Tweedie-Cullen, Ry Y.; Wollscheid, Bernd; Livingstone-Zatchej, Magdalena
Current Proteomics (2007) 4(4): 209-222
Strategy for Comprehensive Identification of Post-translational Modifications in Cellular Proteins, Including Low Abundant Modifications: Application to Glyceraldehyde-3-phosphate Dehydrogenase
Jawon Seo, Jaeho Jeong, Young Mee Kim, Narae Hwang, Eunok Paek, and Kong-Joo Lee
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 587-602
Complications in the Assignment of 14 and 28 Da Mass Shift Detected by Mass Spectrometry as in Vivo Methylation from Endogenous Proteins
Sung Yun Jung, Yehua Li, Yi Wang, Yue Chen, Yingming Zhao, and Jun Qin
ANALYTICAL CHEMISTRY (2008) 80(5): 1721-1729
Highly Robust, Automated, and Sensitive Online TiO2-Based Phosphoproteomics Applied To Study Endogenous Phosphorylation in Drosophila melanogaster
Martijn W. H. Pinkse, Shabaz Mohammed, Joost W. Gouw, Bas van Breukelen, Harmjan R. Vos, and Albert J. R. Heck
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 687-697
Phosphoproteome of Resting Human Platelets
René P. Zahedi, Urs Lewandrowski, Julia Wiesner, Stefanie Wortelkamp, Jan Moebius, Claudia Schütz, Ulrich Walter, Stepan Gambaryan, and Albert Sickmann
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 526-534
The Mycobacterium tuberculosis serine/threonine kinase PknL phosphorylates Rv2175c: Mass spectrometric profiling of the activation loop phosphorylation sites and their role in the recruitment of Rv2175c
Marc J. Canova, Romain Veyron-Churlet, Isabelle Zanella-Cleon, Martin Cohen-Gonsaud, Alain J. Cozzone, Michel Becchi, Laurent Kremer, Virginie Molle
PROTEOMICS (2008) 8(3): 521-533
An efficient method for dephosphorylation of phosphopeptides by cerium oxide
Tan F, Zhang Y, Wang J, Wei J, Cai Y, Qian X.
J Mass Spectrom Early Edition: published 13-Dec-2007
Metal Oxide-Based Enrichment Combined with Gas-Phase Ion-Electron Reactions for Improved Mass Spectrometric Characterization of Protein Phosphorylation
Hye Kyong Kweon and Kristina Håkansson
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 749-755
Phosphoproteome Analysis of E. coli Reveals Evolutionary Conservation of Bacterial Ser/Thr/Tyr Phosphorylation
Boris Macek, Florian Gnad, Boumediene Soufi, Chanchal Kumar, Jesper V.Olsen, Ivan Mijakovic, and Matthias Mann
Mol Cell Proteomics (2008) 7(2): 299-307
Comprehensive Approach to Structural and Functional Glycomics Based on Chemoselective Glycoblotting and Sequential Tag Conversion
Jun-ichi Furukawa, Yasuro Shinohara, Hiromitsu Kuramoto, Yoshiaki Miura, Hideyuki Shimaoka, Masaki Kurogochi, Mika Nakano, and Shin-Ichiro Nishimura
ANALYTICAL CHEMISTRY (2008) 80(4): 1094-1101
Relevance of Protein Isoforms in Proteomic Studies
de la Cadena, Maria P.; Rodriguez-Pineiro, Ana M.; Alvarez-Chaver, Paula; Martinez-Zorzano, Vicenta S.; Rodriguez-Berrocal, Francisco J.
Current Proteomics (2007) 4(4): 235-252
Identification of Protein Targets of 4-Hydroxynonenal Using Click Chemistry for ex Vivo Biotinylation of Azido and Alkynyl Derivatives
Vila A, Tallman KA, Jacobs AT, Liebler DC, Porter NA, Marnett LJ.
Chem Res Toxicol (2008) 21(2): 432-44
Oxidation of proteins: Basic principles and perspectives for blood proteomics
Stefano Barelli, Giorgia Canellini, Lynne Thadikkaran, David Crettaz, Manfredo Quadroni, Joël S. Rossier, Jean-Daniel Tissot, Niels Lion
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 142-157
Proteomic identification of specific glycosyltransferases functionally implicated for the biosynthesis of a targeted glyco-epitope
Chi-Hung Lin, Chia-Wei Lin, Kay-Hooi Khoo
PROTEOMICS (2008) 8(3): 475-483
BlotGlycoABCTM, an Integrated Glycoblotting Technique for Rapid and Large Scale Clinical Glycomics
Yoshiaki Miura, Megumi Hato, Yasuro Shinohara, Hiromitsu Kuramoto, Jun-ichi Furukawa, Masaki Kurogochi, Hideyuki Shimaoka, Mitsuhiro Tada, Kazuaki Nakanishi, Michitaka Ozaki, Satoru Todo, and Shin-Ichiro Nishimura
Mol Cell Proteomics (2008) 7(2): 370-377
Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometry
Julian Vasilescu, Jeffrey C. Smith, Daniel R. Zweitzig, Nicholas J. Denis, Dale S. Haines, Daniel Figeys
Journal of Mass Spectrometry (2008) 43(3): 296-304
Phosphoproteomics: A possible route to novel biomarkers of breast cancer
Metodi Metodiev, Louise Alldridge
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 181-194
Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides
Amanda M. Palumbo, Jetze J. Tepe, and Gavin E. Reid
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 771-779
Contribution of proteomics to the study of the role of cytokeratins in disease and physiopathology
Franck Brouillard, Janine Fritsch, Aleksander Edelman, Mario Ollero
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 264-285
Identification of Protein-Protein Interactions by Mass Spectrometry Coupled Techniques
Abu-Farha M, Elisma F, Figeys D.
Adv Biochem Eng Biotechnol Early Edition: published 29-Jan-2008
Subunit-subunit interactions in the human 26S proteasome
Chuan Chen, Caoxin Huang, Shouhui Chen, Jie Liang, Wenbo Lin, Guifen Ke, Hongxin Zhang, Bing Wang, Jian Huang, Zeguang Han, Lixin Ma, Keke Huo, Xiaoming Yang, Pengyuan Yang, Fuchu He, Tao Tao
PROTEOMICS (2008) 8(3): 508-520
Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis
Mahuya Bose, Brian P. Adams, Randy M. Whittal, Himangshu S. Bose
ELECTROPHORESIS (2008) 29(4): 753-760
Improving yeast two-hybrid screening systems
Manfred Koegl and Peter Uetz
Brief Funct Genomic Proteomic (2007) 6(4): 302-312
PRAS40 and PRR5-Like Protein Are New mTOR Interactors that Regulate Apoptosis
Thedieck K, Polak P, Kim ML, Molle KD, Cohen A, Jenö P, Arrieumerlou C, Hall MN.
PLoS ONE (2007) 2(11): e1217
PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains
Gong W, Zhou D, Ren Y, Wang Y, Zuo Z, Shen Y, Xiao F, Zhu Q, Hong A, Zhou X, Gao X, Li T
Nucl Acids Res (2008) 36(Database issue): D679-83
Quantitative Proteomic Analysis of Protein Complexes: Concurrent Identification of Interactors and Their State of Phosphorylation
Delphine Pflieger, Martin A. Junger, Markus Muller, Oliver Rinner, Hookeun Lee, Peter M. Gehrig, Matthias Gstaiger, and Ruedi Aebersold
Mol Cell Proteomics (2008) 7(2): 326-346
Bacteriome.org--an integrated protein interaction database for E. coli
Su C, Peregrin-Alvarez JM, Butland G, Phanse S, Fong V, Emili A, Parkinson J
Nucl Acids Res (2008) 36(Database issue): D632-6
Proteomic identification of the MYST domain histone acetyltransferase TIP60 (HTATIP) as a co-activator of the myeloid transcription factor C/EBPalpha
Bararia D, Trivedi AK, Zada AA, Greif PA, Mulaw MA, Christopeit M, Hiddemann W, Bohlander SK, Behre G.
Leukemia Early Edition: published 31-Jan-2008
Proteomic identification of ZO-1/2 as a novel scaffold for Src/Csk regulatory circuit
Saito K, Enya K, Oneyama C, Hikita T, Okada M.
Biochem Biophys Res Commun (2008) 366(4): 969-75
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP.
Proc Natl Acad Sci U S A (2008) 105(5): 1454-9
Application of Targeted Quantitative Proteomics Analysis in Human Cerebrospinal Fluid Using a Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Tandem Mass Spectrometer (LC MALDI TOF/TOF) Platform
Sheng Pan, John Rush, Elaine R. Peskind, Douglas Galasko, Kathryn Chung, Joseph Quinn, Joseph Jankovic, James B. Leverenz, Cyrus Zabetian, Catherine Pan, Yan Wang, Jung Hun Oh, Jean Gao, Jianpeng Zhang, Thomas Montine, and Jing Zhang
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 720-730
Absolute Quantification of Monoclonal Antibodies in Biofluids by Liquid Chromatography-Tandem Mass Spectrometry
Charlotte Hagman, Darrell Ricke, Stefan Ewert, Stephan Bek, Rocco Falchetto, and Francis Bitsch
ANALYTICAL CHEMISTRY (2008) 80(4): 1290-1296
Heat-Shock Response in Arabidopsis thaliana Explored by Multiplexed Quantitative Proteomics Using Differential Metabolic Labeling
Magnus Palmblad, Davinia J. Mills, and Laurence V. Bindschedler
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 780-785
Label-Free Comparative Analysis of Proteomics Mixtures Using Chromatographic Alignment of High-Resolution LC-MS Data
Gregory L. Finney, Adele R. Blackler, Michael R. Hoopmann, Jesse D. Canterbury, Christine C. Wu, and Michael J. MacCoss
ANALYTICAL CHEMISTRY (2008) 80(4): 961-971
Quantitative Proteomic Approaches to Investigate the Membrane Proteome in Neuropsychiatric Disorders
Chan, Man K.; Bahn, Sabine
Current Proteomics (2007) 4(3): 131-140
Quantification of NTproBNP in Rat Serum Using Immunoprecipitation and LC/MS/MS: a Biomarker of Drug-Induced Cardiac Hypertrophy
Michael Berna, Lee Ott, Steve Engle, David Watson, Philip Solter, and Bradley Ackermann
ANALYTICAL CHEMISTRY (2008) 80(3): 561-566
A comparison of 2-D chromatography separations using UV and( 18)O quantification of proteins in similar proteomes
Smith JR, Matus I, Greene AS.
J Sep Sci (2008) 31(2): 314-20
Proteomics and naturally occurring animal diseases: Opportunities for animal and human medicine
Mary K. Doherty, Robert J. Beynon, Phillip D. Whitfield
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 135-141
New informatics customer initiative launched by ThermoFisher Scientific, Inc
Expert Review of Proteomics (2007) 4(6): 701-703
Alignment of LC-MS images, with applications to biomarker discovery and protein identification
Mathias Vandenbogaert, Sébastien Li-Thiao-Té, Hans-Michael Kaltenbach, Runxuan Zhang, Tero Aittokallio, Benno Schwikowski
PROTEOMICS (2008) 8(4): 650-672
Application of proteomics technology for analyzing the interactions between host cells and intracellular infectious agents
Mayte Coiras, Emilio Camafeita, María Rosa López-Huertas, Enrique Calvo, Juan Antonio López, José Alcamí
PROTEOMICS (2008) 8(4): 852-873
Soybean Proteomics
Komatsu, Setsuko; Toorchi, Mahmoud; Yukawa, Kiyoshi
Current Proteomics (2007) 4(3): 182-186
Current Status of Computational Approaches for Protein Identification Using Tandem Mass Spectra
Zhang, Xiang; Oh, Cheolhwan; Riley, Catherine P.; Buck, Charles
Current Proteomics (2007) 4(3): 121-130
Ovarian cancer proteomics: Many technologies one goal
Kothandaraman Narasimhan, Zhao Changqing, Mahesh Choolani
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 195-218
Proteomics: from technology development to biomarker applications
Sandra Orchard
Expert Review of Proteomics (2007) 4(6): 709-710
Proteomics of the Human Placenta: Promises and Realities
Robinson JM, Ackerman WE 4th, Kniss DA, Takizawa T, Vandré DD.
Placenta (2008) 29(2): 135-43
Proteomic diagnosis of Sjögren's syndrome
Laura Giusti, Chiara Baldini, Laura Bazzichi, Stefano Bombardieri, Antonio Lucacchini
Expert Review of Proteomics (2007) 4(6): 757-767
Proteomic approach to investigate MRSA
Francois P, Scherl A, Hochstrasser D, Schrenzel J.
Methods Mol Biol (2007) 391: 179-200
Phosphoproteomics: A possible route to novel biomarkers of breast cancer
Metodi Metodiev, Louise Alldridge
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 181-194
Clinical application of proteomics approaches in vascular diseases
Xiao-Li Wang, Alex Fu, Craig Spiro, Hon-Chi Lee
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 238-250
Comparative LC-MS: A landscape of peaks and valleys
Antoine H. P. America, Jan H. G. Cordewener
PROTEOMICS (2008) 8(4): 731-749
Recent advances in plant cell wall proteomics
Elisabeth Jamet, Cécile Albenne, Georges Boudart, Muhammad Irshad, Hervé Canut, Rafael Pont-Lezica
PROTEOMICS (2008) 8(4): 893-908
Possibilities of Two-Dimensional Gel Electrophoresis in the Understanding of Human Disease
Lopez, Jose L.; Bermudez-Crespo, Jose
Current Proteomics (2007) 4(4): 187-197
Identification of Protein-Protein Interactions by Mass Spectrometry Coupled Techniques
Abu-Farha M, Elisma F, Figeys D.
Adv Biochem Eng Biotechnol Early Edition: published 29-Jan-2008
Oxidation of proteins: Basic principles and perspectives for blood proteomics
Stefano Barelli, Giorgia Canellini, Lynne Thadikkaran, David Crettaz, Manfredo Quadroni, Joël S. Rossier, Jean-Daniel Tissot, Niels Lion
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 142-157
Evolutionary medicine: A meaningful connection between omics, disease, and treatment
Mones Abu-Asab, Mohamed Chaouchi, Hakima Amri
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 122-134
Proteomics of Human Bodyfluids: Principles, Methods, and Applications. By Visith Thongboonkerd (Ed.)
Marc A. Reymond
PROTEOMICS (2008) 8(4): 921
Tools for analyzing and predicting N-terminal protein modifications
Thierry Meinnel, Carmela Giglione
PROTEOMICS (2008) 8(4): 626-649
Pfam: a domain-centric method for analyzing proteins and proteomes
Mistry J, Finn R.
Methods Mol Biol (2007) 396: 43-58
Cracking the Enigmatic Linker Histone Code
Godde JS, Ura K.
J Biochem (2008) 143(3): 287-93
Circulating tumor cells: detection, molecular profiling and future prospects
Karine Jacob, Caroline Sollier, Nada Jabado
Expert Review of Proteomics (2007) 4(6): 741-756
Modulation of cancer cell line differentiation: A neglected proteomic analysis with potential implications in pathophysiology, diagnosis, prognosis, and therapy of cancer
Roberto Scatena, Patrizia Bottoni, Bruno Giardina
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 229-237
Proteomics in leptospirosis research: towards molecular diagnostics and vaccine development
Thongboonkerd V.
Expert Rev Mol Diagn (2008) 8(1): 53-61
Proteomic approaches to the analysis of multiprotein signaling complexes
Wei Yang, Hanno Steen, Michael R. Freeman
PROTEOMICS (2008) 8(4): 832-851
Computational Methods and Algorithms for Mass-Spectrometry Based Differential Proteomics
Mavroudi, Seferina; Papadimitriou, Stergios; Kossida, Sophia; Likothanassis, Spyridon D.; Vlahou, Antonia
Current Proteomics (2007) 4(4): 223-234
Kinase signaling pathways as potential targets in the treatment of Parkinson's disease
Elisa Greggio, Andrew Singleton
Expert Review of Proteomics (2007) 4(6): 783-792
Proteomic analysis of liver diseases: molecular mechanisms and biomarker discovery
SantamarÃa E, Muñoz J, Fernández-Irigoyen J, Sesma L, Odriozola L, Corrales FJ.
Mini Rev Med Chem (2008) 8(1): 1-9
Adaptive expression of foreign genes in the clonal variants of bacteria: From proteomics to clinical application
Dinesh D. Sriramulu
PROTEOMICS (2008) 8(4): 882-892
Potential of urinary biomarkers in early bladder cancer diagnosis
Lam T, Nabi G.
Expert Rev Anticancer Ther (2007) 7(8): 1105-1115
Improving yeast two-hybrid screening systems
Manfred Koegl and Peter Uetz
Brief Funct Genomic Proteomic (2007) 6(4): 302-312
Proteomics, networks and connectivity indices
Humberto González-Díaz, Yenny González-Díaz, Lourdes Santana, Florencio M. Ubeira, Eugenio Uriarte
PROTEOMICS (2008) 8(4): 750-778
Informatics for peptide retention properties in proteomic LC-MS
Kosaku Shinoda, Masahiro Sugimoto, Masaru Tomita, Yasushi Ishihama
PROTEOMICS (2008) 8(4): 787-798
Discovery of diagnostic serum biomarkers of gastric cancer using proteomics
Katie Wing-kei Lam, Samuel Chun-lap Lo
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 219-228
Automated technologies and novel techniques to accelerate protein crystallography for structural genomics
Babu A. Manjasetty, Andrew P. Turnbull, Santosh Panjikar, Konrad Büssow, Mark R. Chance
PROTEOMICS (2008) 8(4): 612-625
Mass spectrometry-based proteomics of fungal wall glycoproteins
Yin QY, de Groot PW, de Koster CG, Klis FM.
Trends Microbiol (2008) 16(1): 20-6
Proteomic analysis of Saccharomyces cerevisiae
Trong Khoa Pham, Phillip C Wright
Expert Review of Proteomics (2007) 4(6): 793-813
Immunoproteomics: From biomarker discovery to diagnostic applications
Harold Tjalsma, Renée M. J. Schaeps, Dorine W. Swinkels
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 167-180
Cartilage proteomics: Challenges, solutions and recent advances
Richard Wilson, John F. Bateman
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 251-263
The potential of proteomics for providing new insights into environmental impacts on human health
Sheehan D.
Rev Environ Health (2007) 22(3): 175-94
Identification of accessible human cancer biomarkers using ex vivo chemical proteomic strategies
Philippe Kischel, David Waltregny, Vincent Castronovo
Expert Review of Proteomics (2007) 4(6): 727-739
Contribution of proteomics to the study of the role of cytokeratins in disease and physiopathology
Franck Brouillard, Janine Fritsch, Aleksander Edelman, Mario Ollero
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 264-285
Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis
Xiaogang Jiang, Mingliang Ye, Hanfa Zou
PROTEOMICS (2008) 8(4): 686-705
Circulating markers of biliary malignancy: opportunities in proteomics?
Bonney GK, Craven RA, Prasad R, Melcher AF, Selby PJ, Banks RE.
Lancet Oncol (2008) 9(2): 149-58
Reverse phase protein microarrays for monitoring biological responses
Espina V, Wulfkuhle JD, Calvert VS, Petricoin EF 3rd, Liotta LA.
Methods Mol Biol (2007) 383: 321-36
Protein networking: insights into global functional organization of proteomes
Enrico Pieroni, Sergio de la Fuente van Bentem, Gianmaria Mancosu, Enrico Capobianco, Heribert Hirt, Alberto de la Fuente
PROTEOMICS (2008) 8(4): 799-816
Tandem mass spectrometry in physiology
Pisitkun T, Hoffert JD, Yu MJ, Knepper MA.
Physiology (Bethesda) (2007) 22: 390-400.
Drug resistance in cancer - searching for mechanisms, markers and therapeutic agents
O'Connor R, Clynes M, Dowling P, O'Donovan N, O'Driscoll L.
Expert Opin Drug Metab Toxicol (2007) 3(6): 805-17
Insights into environmental bioremediation by microorganisms through functional genomics and proteomics
Bing Zhao, Chit Laa Poh
PROTEOMICS (2008) 8(4): 874-881
Population proteomics: Investigation of protein diversity in human populations
Dobrin Nedelkov
PROTEOMICS (2008) 8(4): 779-786
Ubiquitin-proteasome system dysfunction in Parkinson's disease: current evidence and controversies
Kah-Leong Lim
Expert Review of Proteomics (2007) 4(6): 769-781
Beyond prostate-specific antigen: alternate serum markers
RamÃrez ML, Nelson EC, Evans CP.
Prostate Cancer Prostatic Dis Early Edition: published 29-Jan-2008
Exploring snake venom proteomes: multifaceted analyses for complex toxin mixtures
Jay W. Fox, Solange M. T. Serrano
PROTEOMICS (2008) 8(4): 909-920
Proteomics, nanotechnology and molecular diagnostics
Christopher J. Johnson, Nikolay Zhukovsky, Anthony E. G. Cass, Judit M. Nagy
PROTEOMICS (2008) 8(4): 715-730
Why 3-D? Gel-based microarrays in proteomics
Alla Yu. Rubina, Alexander Kolchinsky, Alexander A. Makarov, Alexander S. Zasedatelev
PROTEOMICS (2008) 8(4): 817-831
Will current technologies enable dinosaur proteomics?
Gary B Smejkal, Mary H Schweitzer
Expert Review of Proteomics (2007) 4(6): 695-699
Viral proteomics: global evaluation of viruses and their interaction with the host
Kasinath Viswanathan, Klaus Früh
Expert Review of Proteomics (2007) 4(6): 815-829
Target coatings and desorption surfaces in biomolecular MALDI-MS
Simone König
PROTEOMICS (2008) 8(4): 706-714
Human Heart Failure: A Proteomics Perspective
Goel, Arvind; Rakwal, Randeep; Agrawal, Ganesh K.
Current Proteomics (2007) 4(3): 174-181
Phosphorylation site analysis of the anti-inflammatory and mRNA-destabilizing protein tristetraprolin
Heping Cao, Leesa J Deterding, Perry J Blackshear
Expert Review of Proteomics (2007) 4(6): 711-726
Neuroproteomics and the Detection of Regulatory Phosphosites
Mansuy, Isabelle M.; Tweedie-Cullen, Ry Y.; Wollscheid, Bernd; Livingstone-Zatchej, Magdalena
Current Proteomics (2007) 4(4): 209-222
Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS
Takashi Nakazawa, Minoru Yamaguchi, Taka-aki Okamura, Eiji Ando, Osamu Nishimura, Susumu Tsunasawa
PROTEOMICS (2008) 8(4): 673-685
Top-down proteomic analysis by MALDI-TOF profiling: Concentration-independent biomarkers
Gary L. Nelsestuen, Stephen B. Harvey, Yan Zhang, Raj S. Kasthuri, Alan R. Sinaiko, E. Wesley Ely, Gordon R. Bernard, Monika Homoncik, Bernd Jilma
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 158-166
Comparative analysis of MRSA
Takeuchi F, Baba T, Hiramatsu K.
Methods Mol Biol (2007) 391: 153-68
“Product Ion Monitoring” Assay for Prostate-Specific Antigen in Serum Using a Linear Ion-Trap
Vathany Kulasingam, Christopher R. Smith, Ihor Batruch, Alan Buckler, Douglas A. Jeffery, and Eleftherios P. Diamandis
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 640-647
Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses
Gevaert K, Impens F, Van Damme P, Ghesquière B, Hanoulle X, Vandekerckhove J.
FEBS J (2007) 274(24): 6277-89
Automated Proteomics of E. coli via Top-Down Electron-Transfer Dissociation Mass Spectrometry
Maureen K. Bunger, Benjamin J. Cargile, Anne Ngunjiri, Jonathan L. Bundy, and James L. Stephenson, Jr.
ANALYTICAL CHEMISTRY (2008) 80(5): 1459-1467
Strategy for Comprehensive Identification of Post-translational Modifications in Cellular Proteins, Including Low Abundant Modifications: Application to Glyceraldehyde-3-phosphate Dehydrogenase
Jawon Seo, Jaeho Jeong, Young Mee Kim, Narae Hwang, Eunok Paek, and Kong-Joo Lee
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 587-602
Gel-Eluted Liquid Fraction Entrapment Electrophoresis: An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation
Tran JC, Doucette AA.
Anal Chem (2008) 80(5): 1568-73
Assessment of Post-Mortem-Induced Changes to the Mouse Brain Proteome
Hunsucker SW, Solomon B, Gawryluk J, Geiger JD, Vacano GN, Duncan MW, Patterson D.
J Neurochem Early Edition: published 12-Dec-2007
Absolute and Site-Specific Quantification of Protein Phosphorylation Using Integrated Elemental and Molecular Mass Spectrometry: Its Potential To Assess Phosphopeptide Enrichment Procedures
Ana Pereira Navaza, Jorge Ruiz Encinar, Montserrat Carrascal, Joaquín Abi n, and Alfredo Sanz-Medel
ANALYTICAL CHEMISTRY (2008) 80(5): 1777-1787
Membrane Protein Identification: N-Terminal Labeling of Nontryptic Membrane Protein Peptides Facilitates Database Searching
Maria Jansson, Kristofer Wårell, Fredrik Levander, and Peter James
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 659-665
Analysis of Electroblotted Proteins by Mass Spectrometry: Protein Identification after Western Blotting
Jose L. Luque-Garcia, Ge Zhou, Daniel S. Spellman, Tung-Tien Sun, and Thomas A. Neubert
Mol Cell Proteomics (2008) 7(2): 308-314
Target coatings and desorption surfaces in biomolecular MALDI-MS
Simone König
PROTEOMICS (2008) 8(4): 706-714
Comparative LC-MS: A landscape of peaks and valleys
Antoine H. P. America, Jan H. G. Cordewener
PROTEOMICS (2008) 8(4): 731-749
Protein extraction for 2-DE from the lamina of Ecklonia kurome (laminariales): Recalcitrant tissue containing high levels of viscous polysaccharides
Kouhei Nagai, Norishige Yotsukura, Haruka Ikegami, Hajime Kimura, Koichi Morimoto
ELECTROPHORESIS (2008) 29(3): 672-681
Genome-Specific Gas-Phase Fractionation Strategy for Improved Shotgun Proteomic Profiling of Proteotypic Peptides
Alexander Scherl, Scott A. Shaffer, Gregory K. Taylor, Hemantha D. Kulasekara, Samuel I. Miller, and David R. Goodlett
ANALYTICAL CHEMISTRY (2008) 80(4): 1182-1191
Simple and universal tool to remove on-line impurities in mono- or two-dimensional liquid chromatography-mass spectrometry analysis
Hesse AM, Marcelo P, Rossier J, Vinh J.
J Chromatogr A Early Edition: published 4-Jan-2008
Evaluation of strategy for analyzing mouse liver plasma membrane proteome
Chen P, Zhang L, Li X, Wang X, Cao R, Liu Z, Xiong J, Peng X, Wei Y, Ying X, Wang X, Liang S.
Sci China C Life Sci (2007) 50(6): 731-8
Systematic Assessment of the Benefits and Caveats in Mining Microbial Post-Translational Modifications from Shotgun Proteomic Data: The Response of Shewanella oneidensis to Chromate Exposure
Melissa R. Thompson, Dorothea K. Thompson, and Robert L. Hettich
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 648-658
Top-down proteomic analysis by MALDI-TOF profiling: Concentration-independent biomarkers
Gary L. Nelsestuen, Stephen B. Harvey, Yan Zhang, Raj S. Kasthuri, Alan R. Sinaiko, E. Wesley Ely, Gordon R. Bernard, Monika Homoncik, Bernd Jilma
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(2): 158-166
Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides
Amanda M. Palumbo, Jetze J. Tepe, and Gavin E. Reid
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 771-779
Microscale solution IEF combined with 2-D DIGE substantially enhances analysis depth of complex proteomes such as mammalian cell and tissue extracts
Mee-Jung Han, Meenhard Herlyn, Aron B. Fisher, David W. Speicher
ELECTROPHORESIS (2008) 29(3): 695-705
Impact of sample preparation in peptide/protein profiling in human serum by MALDI-TOF mass spectrometry
Aresta A, Calvano CD, Palmisano F, Zambonin CG, Monaco A, Tommasi S, Pilato B, Paradiso A.
J Pharm Biomed Anal (2008) 46(1): 157-64
Global Amine and Acid Functional Group Modification of Proteins
Casey J. Krusemark, Jonathan T. Ferguson, Craig D. Wenger, Neil L. Kelleher, and Peter J. Belshaw
ANALYTICAL CHEMISTRY (2008) 80(3): 713-720
Evaluation of Microwave-Accelerated Residue-Specific Acid Cleavage for Proteomic Applications
Stephen Swatkoski, Peter Gutierrez, Colin Wynne, Alexey Petrov, Jonathan D. Dinman, Nathan Edwards, and Catherine Fenselau
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 579-586
Smart Hydrogel Particles: Biomarker Harvesting: One-Step Affinity Purification, Size Exclusion, and Protection against Degradation
Luchini A, Geho DH, Bishop B, Tran D, Xia C, Dufour RL, Jones CD, Espina V, Patanarut A, Zhou W, Ross MM, Tessitore A, Iii EF, Liotta LA.
Nano Lett (2008) 8(1): 350-61
Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis
Xiaogang Jiang, Mingliang Ye, Hanfa Zou
PROTEOMICS (2008) 8(4): 686-705
Tissue profiling MALDI mass spectrometry reveals prominent calcium-binding proteins in the proteome of regenerative MRL mouse wounds
Caldwell RL, Opalenik SR, Davidson JM, Caprioli RM, Nanney LB.
Wound Repair Regen Early Edition: published 13-Dec-2007
Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis
Mahuya Bose, Brian P. Adams, Randy M. Whittal, Himangshu S. Bose
ELECTROPHORESIS (2008) 29(4): 753-760
Stoichiometry and Absolute Quantification of Proteins with Mass Spectrometry Using Fluorescent and Isotope-labeled Concatenated Peptide Standards
Dhaval Nanavati, Marjan Gucek, Jacqueline L. S. Milne, Sriram Subramaniam, and Sanford P. Markey
Mol Cell Proteomics (2008) 7(2): 442-447
High-resolution 2-DE for resolving proteins, protein adducts and complexes in plasma
Giovanni Candiano, Laura Santucci, Andrea Petretto, Barbara Pavone, Piero Del Boccio, Luca Musante, Maurizio Bruschi, Giorgio Federici, Rosanna Gusmano, Andrea Urbani, Gian M. Ghiggeri
ELECTROPHORESIS (2008) 29(3): 682-694
A Sulfated, Phosphorylated 7 kDa Secreted Peptide Characterized by Direct Analysis of Cell Culture Media
Steven W. Taylor, Chengzao Sun, Amy Hsieh, Nancy L. Andon, and Soumitra S. Ghosh
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 795-802
New prospects for proteomics - electron-capture (ECD) and electron-transfer dissociation (ETD) fragmentation techniques and combined fractional diagonal chromatography (COFRADIC)
Appella E, Anderson CW.
FEBS J (2007) 274(24): 6255
Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis
Takeshi Masuda, Masaru Tomita, and Yasushi Ishihama
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 731-740
Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS
Takashi Nakazawa, Minoru Yamaguchi, Taka-aki Okamura, Eiji Ando, Osamu Nishimura, Susumu Tsunasawa
PROTEOMICS (2008) 8(4): 673-685
Mass Imaging and Identification of Biomolecules with MALDI-QIT-TOF-Based System
Shuichi Shimma, Yuki Sugiura, Takahiro Hayasaka, Nobuhiro Zaima, Mineo Matsumoto, and Mitsutoshi Setou
ANALYTICAL CHEMISTRY (2008) 80(3): 878-885
Optimization of Activity-Based Probes for Proteomic Profiling of Histone Deacetylase Complexes
Salisbury CM, Cravatt BF.
J Am Chem Soc (2008) 130(7): 2184-94
Identification of Protein Targets of 4-Hydroxynonenal Using Click Chemistry for ex Vivo Biotinylation of Azido and Alkynyl Derivatives
Vila A, Tallman KA, Jacobs AT, Liebler DC, Porter NA, Marnett LJ.
Chem Res Toxicol (2008) 21(2): 432-44
Integrating spatially resolved three-dimensional MALDI IMS with in vivo magnetic resonance imaging
Sinha TK, Khatib-Shahidi S, Yankeelov TE, Mapara K, Ehtesham M, Cornett DS, Dawant BM, Caprioli RM, Gore JC.
Nat Methods (2008) 5(1): 57-9
Toward chromatographic analysis of interacting protein networks
Liu X, Yang WC, Gao Q, Regnier F.
J Chromatogr A (2008) 1178(1-2): 24-32
Identification of redox-active cell-surface proteins by mechanism-based kinetic trapping
Schwertassek U, Weingarten L, Dick TP.
Sci STKE (2007) 2007(417): pl8
Matrix-assisted laser desorption/ionization signal enhancement of peptides by picolinamidination of amino groups
Jong-Seo Kim, Ji-Hyun Kim, Hie-Joon Kim
Rapid Communications in Mass Spectrometry (2008) 22(4): 495-502
On-target sample preparation of 4-sulfophenyl isothiocyanate-derivatized peptides using AnchorChip Targets
Xumin Zhang, Adelina Rogowska-Wrzesinska, Peter Roepstorff
Journal of Mass Spectrometry (2008) 43(3): 346-359
High-Throughput Analysis of Rat Liver Plasma Membrane Proteome by a Nonelectrophoretic In-Gel Tryptic Digestion Coupled with Mass Spectrometry Identification
Rui Cao, QuanYuan He, Jian Zhou, QuanZe He, Zhen Liu, XianChun Wang, Ping Chen, Jingyun Xie, and SongPing Liang
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 535-545
An efficient method for dephosphorylation of phosphopeptides by cerium oxide
Tan F, Zhang Y, Wang J, Wei J, Cai Y, Qian X.
J Mass Spectrom Early Edition: published 13-Dec-2007
Resolving and Identifying Protein Components of Plant Mitochondrial Respiratory Complexes Using Three Dimensions of Gel Electrophoresis
Etienne H. Meyer, Nicolas L. Taylor, and A. Harvey Millar
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 786-794
Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics
McLafferty FW, Breuker K, Jin M, Han X, Infusini G, Jiang H, Kong X, Begley TP.
FEBS J (2007) 274(24): 6256-68
Protein Arrays on Patterned Porous Gold Substrates Interrogated with Mass Spectrometry: Detection of Peptides in Plasma
Kenyon M. Evans-Nguyen, Sheng-Ce Tao, Heng Zhu, and Robert J. Cotter
ANALYTICAL CHEMISTRY (2008) 80(5): 1448-1458
Comparative proteomics and difference gel electrophoresis
Minden J.
Biotechniques (2007) 43(6): 739, 741, 743 passim
Shell-core imprinted polyacrylamide crosslinked chitosan for albumin removal from plasma
Okutucu B, Zihnioglu F, Telefoncu A.
J Biomed Mater Res A (2008) 84(3): 842-5
Automated technologies and novel techniques to accelerate protein crystallography for structural genomics
Babu A. Manjasetty, Andrew P. Turnbull, Santosh Panjikar, Konrad Büssow, Mark R. Chance
PROTEOMICS (2008) 8(4): 612-625
A novel probe for chemiluminescent image detection of proteins in two-dimensional gel electrophoresis
Jia Liu, Jin Ouyang, Willy R. G. Baeyens, Joris R. Delanghe, Zhenzhen Wang, Jinxiu Liu, Huiying Zhang
ELECTROPHORESIS (2008) 29(3): 716-725
Proteomic analysis of RCL2 paraffin-embedded tissues
Bellet V, Boissière F, Bibeau F, Desmetz C, Berthe M, Rochaix P, Maudelonde T, Mangé A, Solassol J.
J Cell Mol Med Early Edition: published 10-Dec-2007
Combinatorial synthesis of peptide arrays onto a microchip
Beyer M, Nesterov A, Block I, König K, Felgenhauer T, Fernandez S, Leibe K, Torralba G, Hausmann M, Trunk U, Lindenstruth V, Bischoff FR, Stadler V, Breitling F.
Science (2007) 318(5858): 1888
A Versatile Nanotrap for Biochemical and Functional Studies with Fluorescent Fusion Proteins
Ulrich Rothbauer, Kourosh Zolghadr, Serge Muyldermans, Aloys Schepers,M. Cristina Cardoso, and Heinrich Leonhardt
Mol Cell Proteomics (2008) 7(2): 282-289
Complications in the Assignment of 14 and 28 Da Mass Shift Detected by Mass Spectrometry as in Vivo Methylation from Endogenous Proteins
Sung Yun Jung, Yehua Li, Yi Wang, Yue Chen, Yingming Zhao, and Jun Qin
ANALYTICAL CHEMISTRY (2008) 80(5): 1721-1729
Use of DNA Ladders for Reproducible Protein Fractionation by Sodium Dodecyl Sulfate−Polyacrylamide Gel Electrophoresis (SDS−PAGE) for Quantitative Proteomics
Guoan Zhang, David Fenyö, and Thomas A. Neubert
JOURNAL OF PROTEOME RESEARCH (2008) 7(02): 678-686
Evaluation of reproducibility of protein identification results after multidimensional human serum protein separation
Daniel Stalder, André Haeberli, Manfred Heller
PROTEOMICS (2008) 8(3): 414-424
Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking
Xin Guo, Pradipta Bandyopadhyay, Birgit Schilling, Malin M. Young, Naoaki Fujii, Tiba Aynechi, R. Kiplin Guy, Irwin D. Kuntz, and Bradford W. Gibson
ANALYTICAL CHEMISTRY (2008) 80(4): 951-960
The Invisible Proteome: How to Capture the Low-Abundance Proteins Via Combinatorial Ligand Libraries
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Nature (2007) 450(7172): 991-1000
HUPO Brain Proteome Project: Toward a Code of Conduct
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Mol Cell Proteomics (2008) 7(2): 457
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Nature (2007) 450(7172): 973-82