My proteomics journal watch - year 2004 Jul-Dec [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 ]

General Application    Basic Science Studies    Disease research    Clinical application    Pharmacogenomics Protein-protein interaction    Network/pathway reconstruction and analysis Structural genomics Technical developments    Protein expression techniques    2D gel; Protein purification and chromatographic techniques    Mass spectrometry    Protein-protein interaction study    Protein function study    Post-translational modification study Data analysis Software Database * Protein chip related articles are put under the microarray section of My functional genomics journal watch

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General

1. Cottingham K. Integrated proteomics systems bring the pieces together. Anal Chem. 2004 Sep 1;76(17):331A-335A. [PubMed]
2. Steen H, Mann M. The abc's (and xyz's) of peptide sequencing. Nat Rev Mol Cell Biol. 2004 Sep;5(9):699-711. [PubMed]
   

Application

1. Rose K, Bougueleret L, Baussant T, Bohm G, Botti P, Colinge J, Cusin I, Gaertner H, Gleizes A, Heller M, Jimenez S, Johnson A, Kussmann M, Menin L, Menzel C, Ranno F, Rodriguez-Tome P, Rogers J, Saudrais C, Villain M, Wetmore D, Bairoch A, Hochstrasser D. Industrial-scale proteomics: From liters of plasma to chemically synthesized proteins. Proteomics. 2004 Jul;4(7):2125-50. [PubMed]
   

Basic Science Studies

1. Karlsson C, Korayem AM, Scherfer C, Loseva O, Dushay MS, Theopold U. Proteomic analysis of the drosophila larval hemolymph clot. J Biol Chem. 2004 Oct 4;. [Epub ahead of print][PubMed]
2. Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol. 2004 Sep;22(9):1139-45. [PubMed]
3. Jalili PR, Dass C. Proteome analysis in the bovine adrenal medulla using liquid chromatography with tandem mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(17):1877-84. [PubMed]
4. Kho Y, Kim SC, Jiang C, Barma D, Kwon SW, Cheng J, Jaunbergs J, Weinbaum C, Tamanoi F, Falck J, Zhao Y. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. roc Natl Acad Sci U S A. 2004 Aug 24;101(34):12479-84. [PubMed]
5. Bredemeyer AJ, Lewis RM, Malone JP, Davis AE, Gross J, Townsend RR, Ley TJ. A proteomic approach for the discovery of protease substrates. Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11785-90. [PubMed]
6. Kameyama A, Kaneda Y, Yamanaka H, Yoshimine H, Narimatsu H, Shinohara Y. Detection of Oligosaccharides Labeled with Cyanine Dyes Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem. 2004 Aug 1;76(15):4537-4542. [PubMed]
7. Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG. System-based proteomic analysis of the interferon response in human liver cells. Genome Biol. 2004;5(8):R54. [PubMed]
8. Allet N, Barrillat N, Baussant T, Boiteau C, Botti P, Bougueleret L, Budin N, Canet D, Carraud S, Chiappe D, Christmann N, Colinge J, Cusin I, Dafflon N, Depresle B, Fasso I, Frauchiger P, Gaertner H, Gleizes A, Gonzalez-Couto E, Jeandenans C, Karmime A, Kowall T, Lagache S, Mahe E, Masselot A, Mattou H, Moniatte M, Niknejad A, Paolini M, Perret F, Pinaud N, Ranno F, Raimondi S, Reffas S, Regamey PO, Rey PA, Rodriguez-Tome P, Rose K, Rossellat G, Saudrais C, Schmidt C, Villain M, Zwahlen C. In vitro and in silico processes to identify differentially expressed proteins. Proteomics. 2004 Aug;4(8):2333-51. [PubMed]   
9. Durr E, Yu J, Krasinska KM, Carver LA, Yates JR, Testa JE, Oh P, Schnitzer JE. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol. 2004 Aug;22(8):985-92. [PubMed]
10. Fountoulakis M. Application of proteomics technologies in the investigation of the brain. Mass Spectrom Rev. 2004 Jul-Aug;23(4):231-58. [PubMed]
11. Warnock DE, Fahy E, Taylor SW. Identification of protein associations in organelles, using mass spectrometry-based proteomics. Mass Spectrom Rev. 2004 Jul-Aug;23(4):259-80. [PubMed]
12. Zhou Y, Gu G, Goodlett DR, Zhang T, Pan C, Montine TJ, Montine KS, Aebersold RH, Zhang J. Analysis of alpha -synuclein-associated proteins by quantitative proteomics. J Biol Chem. 2004 Jul 1;. [Epub ahead of print][PubMed]
13. Colland F, Jacq X, Trouplin V, Mougin C, Groizeleau C, Hamburger A, Meil A, Wojcik J, Legrain P, Gauthier JM. Functional proteomics mapping of a human signaling pathway. Genome Res. 2004 Jul;14(7):1324-32. [PubMed]
14. Ranish JA, Hahn S, Lu Y, Yi EC, Li XJ, Eng J, Aebersold R. Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet. 2004 Jul;36(7):707-13. [PubMed]
15. Yu LR, Conrads TP, Uo T, Kinoshita Y, Morrison RS, Lucas DA, Chan KC, Blonder J, Issaq HJ, Veenstra TD. Global analysis of the cortical neuron proteome. Mol Cell Proteomics. 2004 Jun 30;. [Epub ahead of print] [PubMed]

Disease research

1. Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR 3rd, Winzeler EA. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004 Nov;14(11):2308-18. [PubMed]
2. Pan TL, Wang PW, Huang CC, Goto S, Chen CL. Expression, by functional proteomics, of spontaneous tolerance in rat orthotopic liver transplantation. Immunology. 2004 Sep;113(1):57-64. [PubMed]
3. Liao L, Cheng D, Wang J, Duong DM, Losik TG, Gearing M, Rees HD, Lah JJ, Levey AI, Peng J. Proteomic characterization of postmortem amyloid plaques isolated by laser capture microdissection. J Biol Chem. 2004 Aug 27;279(35):37061-8. [PubMed]
4. Lim MS, Elenitoba-Johnson KS. Proteomics in pathology research. Lab Invest. 2004 Aug 16;. [Epub ahead of print] [PubMed]
5. Keay SK, Szekely Z, Conrads TP, Veenstra TD, Barchi JJ Jr, Zhang CO, Koch KR, Michejda CJ. An antiproliferative factor from interstitial cystitis patients is a frizzled 8 protein-related sialoglycopeptide. Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11803-8.[PubMed]
6. Gravett MG, Novy MJ, Rosenfeld RG, Reddy AP, Jacob T, Turner M, McCormack A, Lapidus JA, Hitti J, Eschenbach DA, Roberts CT Jr, Nagalla SR. Diagnosis of intra-amniotic infection by proteomic profiling and identification of novel biomarkers. JAMA. 2004 Jul 28;292(4):462-9. [PubMed]
7. Kraemer KH. From proteomics to disease. Nat Genet. 2004 Jul;36(7):677-8. [PubMed]
   

Clinical application

1. Morris K. Proteomics approach could produce blood test for AIDS dementia. Lancet Neurol. 2003 Aug;2(8):455. [PubMed]
2. Rodland KD. Proteomics and cancer diagnosis: the potential of mass spectrometry. Clin Biochem. 2004 Jul;37(7):579-583. [PubMed]
   

   Pharmacogenomics

Protein-protein interaction

1. Baudot A, Jacq B, Brun C. A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biol. 2004;5(10):R76. [PubMed]
2. Luker KE, Smith MC, Luker GD, Gammon ST, Piwnica-Worms H, Piwnica-Worms D. Kinetics of regulated protein-protein interactions revealed with firefly luciferase complementation imaging in cells and living animals. Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12288-93.[PubMed]
   

Network/pathway reconstruction and analysis

1. Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol. 2004 Sep;22(9):1139-45. [PubMed]
2. Yamanishi Y, Vert JP, Kanehisa M. Protein network inference from multiple genomic data: a supervised approach.  Bioinformatics. 2004 Aug 4;20 Suppl 1:I363-I370. [PubMed]
3. Gagneur J, Krause R, Bouwmeester T, Casari G. Modular decomposition of protein-protein interaction networks. Genome Biol. 2004;5(8):R57. [PubMed]

Structural genomics

1. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N. High-Throughput Computational and Experimental Techniques in Structural Genomics. Genome Res. 2004 Oct;14(10B):2145-54. [PubMed]
2. Lundstrom K. Structural genomics on membrane proteins: mini review. Comb Chem High Throughput Screen. 2004 Aug;7(5):431-9.[PubMed]
   

Technical developments

1. Resing KA, Meyer-Arendt K, Mendoza AM, Aveline-Wolf LD, Jonscher KR, Pierce KG, Old WM, Cheung HT, Russell S, Wattawa JL, Goehle GR, Knight RD, Ahn NG. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem. 2004 Jul 1;76(13):3556-68. [PubMed]
   

Protein expression techniques

1. Spirin AS. High-throughput cell-free systems for synthesis of functionally active proteins. Trends Biotechnol. 2004 Oct;22(10):538-45. [PubMed]
   

2D gel; Protein purification and chromatographic techniques

1. Wheeler AR, Moon H, Kim CJ, Loo JA, Garrell RL. Electrowetting-Based Microfluidics for Analysis of Peptides and Proteins by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem. 2004 Aug 15;76(16):4833-4838. [PubMed]
2. Kaczmarek K, Walczak B, De Jong S, Vandeginste BG. Preprocessing of two-dimensional gel electrophoresis images. Proteomics. 2004 Aug;4(8):2377-89. [PubMed]
3. Jorgensen CS, Jagd M, Sorensen BK, McGuire J, Barkholt V, Hojrup P, Houen G. Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate-polyacrylamide gels and polyvinyldifluoride membranes. Anal Biochem. 2004 Jul 1;330(1):87-97. [PubMed]
4. Fievet J, Dillmann C, Lagniel G, Davanture M, Negroni L, Labarre J, De Vienne D. Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis. Proteomics. 2004 Jul;4(7):1939-49. [PubMed]
5. Zhang J, Hu H, Gao M, Yang P, Zhang X. Comprehensive two-dimensional chromatography and capillary electrophoresis coupled with tandem time-of-flight mass spectrometry for high-speed proteome analysis. Electrophoresis. 2004 Jul;25(14):2374-83. [PubMed]  

   Mass spectrometry

Protein-protein interaction study

1. Guo D, Hazbun TR, Xu XJ, Ng SL, Fields S, Kuo MH. A tethered catalysis, two-hybrid system to identify protein-protein interactions requiring post-translational modifications. Nat Biotechnol. 2004 Jul;22(7):888-92. [PubMed]

   Protein function study

Post-translational modification study

1. Kho Y, Kim SC, Jiang C, Barma D, Kwon SW, Cheng J, Jaunbergs J, Weinbaum C, Tamanoi F, Falck J, Zhao Y. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. roc Natl Acad Sci U S A. 2004 Aug 24;101(34):12479-84. [PubMed]
   

Data analysis

1. Kreil DP, Karp NA, Lilley KS. DNA microarray normalization methods can remove bias from differential protein expression analysis of 2-D difference gel electrophoresis results. Bioinformatics. 2004 Sep 1; [PubMed]
2. Orchard S, Taylor CF, Hermjakob H, Weimin-Zhu, Julian RK Jr, Apweiler R. Advances in the development of common interchange standards for proteomic data. Proteomics. 2004 Aug;4(8):2363-5. [PubMed]
3. Anderle M, Roy S, Lin H, Becker C, Joho K. Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. Bioinformatics. 2004 Jul 29 [Epub ahead of print] [PubMed]
4. Li L, Umbach DM, Terry P, Taylor JA. Application of the GA/KNN method to SELDI proteomics data. Bioinformatics. 2004 Jul 1;20(10):1638-40. [PubMed]
5. Li XJ, Pedrioli PG, Eng J, Martin D, Yi EC, Lee H, Aebersold R. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem. 2004 Jul 1;76(13):3856-60. [PubMed]
6. Colinge J, Masselot A, Cusin I, Mahe E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey PA, Bougueleret L. High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics. 2004 Jul;4(7):1977-84. [PubMed]
7. White CN, Chan DW, Zhang Z. Bioinformatics strategies for proteomic profiling. Clin Biochem. 2004 Jul;37(7):636-641. [PubMed]

Software

Database

1. Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol. 2004 Nov;22(11):1459-66. [PubMed]
2. Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF, Carroll K, Evans C, Whetton AD, Hart S, Stead D, Yin Z, Brown AJ, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW. PEDRo: A database for storing, searching and disseminating experimental proteomics data. BMC Genomics. 2004 Sep 17 [Epub ahead of print] [PubMed]
3. Hoogland C, Mostaguir K, Sanchez JC, Hochstrasser DF, Appel RD. SWISS-2DPAGE, ten years later. Proteomics. 2004 Aug;4(8):2352-6. [PubMed]
4. Bluggel M, Bailey S, Korting G, Stephan C, Reidegeld KA, Thiele H, Apweiler R, Hamacher M, Meyer HE. Towards data management of the HUPO Human Brain Proteome Project pilot phase. Proteomics. 2004 Aug;4(8):2361-2. [PubMed]
   
5. Pons JL, Malliavin TE, Tramesel D, Delsuc MA. NMRb: a web-site repository for raw NMR data-sets. Bioinformatics. 2004 Jul 29 [Epub ahead of print] [PubMed]
6. Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R. The International Protein Index: An integrated database for proteomics experiments. Proteomics. 2004 Jul;4(7):1985-8. [PubMed]
7. Huang TW, Tien AC, Huang WS, Lee YC, Peng CL, Tseng HH, Kao CY, Huang CY. POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics. 2004 Jun 24 [Epub ahead of print] [PubMed]