My proteomics journal watch - year 2001 [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 ]
General
A Trends guide to proteomics II
2-d gel electrophoresis and mass spectroscopy applications in expression profiling
Protein-protein interaction
Application
Structural genomics
Technical issues
Software
Database

* Protein chip related articles are put under the microarray section of My functional genomics journal watch

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General

  1. Marshall E. PROTEOMICS: A Physicist-Turned-Biologist. Science. 2001 Dec 7;294(5549):2085. [PubMed]
  2. Service RF. PROTEOMICS: Searching for Recipes for Protein Chips.  Science. 2001 Dec 7;294(5549):2080-2082. [PubMed]
  3. Service RF. PROTEOMICS: Proteomics 2.0: The View Ahead.  Science. 2001 Dec 7;294(5549):2076. [PubMed]
  4. Service RF. PROTEOMICS: High-Speed Biologists Search for Gold in Proteins. Science. 2001 Dec 7;294(5549):2074-2077. [PubMed]
  5. Leung YF, Pang CP. Trends in proteomics. Trends Biotechnol. 2001 Dec;19(12):480-2. [PubMed]
  6. Mrowka R, Patzak A, Herzel H. Is There a Bias in Proteome Research? Genome Res. 2001 Dec; 11:1971-1973 [PubMed]
  7. Hanash S. A meeting of minds in proteomics. Proteomics. 2001 Dec;1(12):1475-8. [PubMed]
  8. Brock A, Huang S. Proteomics in context. Trends Biotechnol. 2001 Nov;19(11):435. [PubMed]
  9. Wickware P, Smaglik P. Proteomics technology: Character references. Nature. 2001 Oct 25;413(6858):869-875. [PubMed]
  10. Wood DW. Conquering the proteome: complexity, cooperation and commerce. Trends Biotechnol. 2001 Oct; 19:375-428 [PubMed]
  11. Le Naour F. Contribution of proteomics to tumor immunology. Proteomics. 2001 Oct;1(10):1295-302. [PubMed]
  12. Dua K, Williams TM, Beretta L. Translational control of the proteome: relevance to cancer. Proteomics. 2001 Oct;1(10):1191-9. [PubMed]
  13. Peng J, Gygi SP. Proteomics: the move to mixtures. J Mass Spectrom. 2001 Oct;36(10):1083-1091. [PubMed]
  14. Bussow K. Proteins in gels, computers, crystals and camels. Trends Biotechnol. 2001. Sep; 19:328-329. [PubMed]
  15. Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M. Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function.  Genome Res. 2001 Sep;11(9):1463-1468. [PubMed]
  16. Dove A.  Proteomics: Basic research climbs aboard. Nat Med. 2001 Sep;7(9):984. [PubMed]
  17. de Bono S.  Budding proteomics.  Trends Biochem Sci. 2001 Sep;26(9):532. [PubMed]
  18. MacCoss MJ, Yates III JR.  Proteomics: analytical tools and techniques.  Curr Opin Clin Nutr Metab Care. 2001 Sep;4(5):369-75. [PubMed]
  19. Matthews DE.  What is more exciting than 'genomics'? 'Proteomics'.    Curr Opin Clin Nutr Metab Care. 2001 Sep;4(5):339. [PubMed]
  20. Clinical Proteomics Program Announced.  J Natl Cancer Inst. 2001 Aug 15;93(16):1203. [PubMed]
  21. Hebestreit HF.  Proteomics: an holistic analysis of nature's proteins [Review]. Curr Opin Pharmacol 2001 Aug; 1: 513-520 [PubMed]
  22. Gupta P, Guglani L. Proteomics: challenge for the new millennium.   Indian Pediatr. 2001 Aug;38(8):875-83 [PubMed]
  23. Sperling K. From proteomics to genomics. Electrophoresis. 2001 Aug;22(14):2835-7. [PubMed]
  24. Riggs L, Sioma C, Regnier FE. Automated signature peptide approach for proteomics. J Chromatogr A. 2001 Jul 27;924(1-2):359-68. [PubMed]
  25. Handley J. Proteomics systems emerge. Anal Chem. 2001 Jul 1;73(13):379A-383A. [PubMed]
  26. Brower V. Proteomics: biology in the post-genomic era: Companies all over the world rush to lead the way in the new post-genomics race. EMBO Rep. 2001 Jul;2(7):558-60. [PubMed]
  27. Lawler S.  Proteomics moves into the spotlight. Trends Cell Biol. 2001 Jul;11(7):284. [PubMed]
  28. Naaby-Hansen S, Waterfield MD, Cramer R. Proteomics - post-genomic cartography to understand gene function. Trends Pharmacol Sci. 2001 Jul;22(7):376-84. [PubMed]
  29. Vosseller K, Wells L, Hart GW. Nucleocytoplasmic O-glycosylation: O-GlcNAc and functional proteomics. Biochimie. 2001 Jul;83(7):575-81. [PubMed]
  30. van Wijk KJ. Challenges and prospects of plant proteomics. Plant Physiol. 2001 Jun;126(2):501-8. [PubMed]
  31. Lee KH. Proteomics: a technology-driven and technology-limited discovery science. Trends Biotechnol. 2001 June; 19:217-222 [PubMed]
  32. Jain KK. Proteomics: new technologies and their applications. Drug Discov Today. 2001 May 1;6(9):457-459. [PubMed]
  33. Husi H, Grant SG. Proteomics of the nervous system. Trends Neurosci. 2001 May;24(5):259-66. [PubMed]
  34. Grandi G. Antibacterial vaccine design using genomics and proteomics. Trends Biotechnol. 2001. May; 19:181-188. [PubMed]
  35. Abbott A. Swiss proteomics company aims to make big impact. Nature. 2001 Apr 19;410(6831):856. [PubMed]
  36. The proteome isn't genome II. Nature. 2001 Apr 12;410(6830):725. [PubMed]
  37. Neurath H.  From proteases to proteomics. Protein Sci. 2001 Apr;10(4):892-904 [PubMed]
  38. Wang Z, Moult J.  SNPs, protein structure, and disease. Hum Mutat. 2001 Apr;17(4):263-70. [PubMed]
  39. Kumar A, Snyder M. Emerging technologies in yeast genomics. Nat Rev Genet. 2001 Apr;2(4):302-12. [PubMed]
  40. Williams M. Genomics, proteomics and gnomics.  Curr Opin Investig Drugs. 2001 Apr;2(4):437-9 [PubMed]
  41. Heinrich-Hirsch B, Madle S, Oberemm A, Gundert-Remy U. The use of toxicodynamics in risk assessment. Toxicol Lett. 2001 Mar 31;120(1-3):131-41. [PubMed]
  42. Lepleya RA, Yoshida M, Loo JA.  Proteomics as a tool in the pharmaceutical drug design process.  Curr Pharm Des. 2001 Mar;7(4):291-310. [PubMed]
  43. Rohlff C. Proteomics in neuropsychiatric disorders. Int J Neuropsychopharmacol. 2001 Mar;4(1):93-102. [PubMed]
  44. Tonella L, Hoogland C, Binz PA, Appel RD, Hochstrasser DF, Sanchez JC. New perspectives in the Escherichia coli proteome investigation . Proteomics. 2001 Mar;1(3):409-23. [PubMed]
  45. Human Genome Project Publications:
  46. Pellegrini M.  Computational methods for protein function analysis. Curr Opin Chem Biol. 2001 Feb 1;5(1):46-50. [PubMed]
  47. Marcotte EM. Measuring the dynamics of the proteome. Genome Res. 2001 Feb; 11: 191-193. [PubMed]
  48. Miklos GL, Maleszka R. Protein functions and biological contexts . Proteomics. 2001 Feb;1(2):169-78. [PubMed]
  49. Hirabayashi J, Arata Y, Kasai K. Glycome project: concept, strategy and preliminary application to Caenorhabditis elegans.  Proteomics. 2001 Feb;1(2):295-303. [PubMed]
  50. Palzkill T. Impending Doom: Antibiotic exposure and bacterial gene expression. Genome Res. 2001 Jan; 11: 1-2 [PubMed]
  51. Anderson NG, Matheson A, Anderson NL. Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology.  Proteomics. 2001 Jan;1(1):3-12. [PubMed]
  52. Miklos GL, Maleszka R.. Integrating molecular medicine with functional proteomics: Realities and expectations. Proteomics 2001. Jan; 1:30-41 [PubMed]
  53. Figeys D, Pinto D. Proteomics on a chip: promising developments. Electrophoresis. 2001 Jan;22(2):208-16. [PubMed]
  54. Miklos GL, Maleszka R. Protein functions and biological contexts. Electrophoresis. 2001;22(4):169-78. [PubMed]
  55. Herrmann PC, Liotta LA, Petricoin III EF. Cancer proteomics: The state of the art. Dis Markers. 2001;17(2):49-57. [PubMed]
  56. Dongre AR, Opiteck G, Cosand WL, Hefta SA. Proteomics in the post-genome age. Biopolymers. 2001;60(3):206-11. [PubMed]
  57. Corthals G L, Nelson P S. Large-scale proteomics and its future impact on medicine. Pharmacogenomics J. 2001;1(1):15-9. [PubMed]

A Trends guide to proteomics II

  1. A TRENDS Guide to Proteomics II.   2001 Oct
    1. Blackstock W. et al. A boundless future for proteomics? Trends Biotechnol. 2001:19:S1-S2 [PubMed][pdf]
    2. Herbert BR, Harry JL, Packer NH, Gooley AA, Pedersen SK, Williams KL. What place for polyacrylamide in proteomics? Trends Biotechnol. 2001:19:S3-S9 [PubMed][pdf]
    3. Moseley MA. Current trends in differential expression proteomics: isotopically coded tags. Trends Biotechnol. 2001:19:S10-S16 [PubMed][pdf]
    4. Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS. Matching peptide mass spectra to EST and genomic DNA databases. Trends Biotechnol. 2001:19:S17-S22 [PubMed][pdf]
    5. Ito T, Chiba T, Yoshida M. Exploring the protein interactome using comprehensive two-hybrid projects. Trends Biotechnol. 2001:19:S23-S27 [PubMed][pdf]
    6. Natsume T, Nakayama H, Isobe T. BIA–MS–MS: biomolecular interaction analysis for functional proteomics. Trends Biotechnol. 2001:19:S28-S33 [PubMed][pdf]
    7. Zhou H, Roy S, Schulman H, Natan MJ. Solution and chip arrays in protein profiling. Trends Biotechnol. 2001:19:S34-S39 [PubMed][pdf]
    8. Simpson RJ, Dorow DS. Cancer proteomics: from signaling networks to tumor markers. Trends Biotechnol. 2001:19:S40-S48 [PubMed][pdf]
    9. Grant SG, Husi H. Proteomics of multiprotein complexes: answering fundamental questions in neuroscience. Trends Biotechnol. 2001:19:S49-S54 [PubMed][pdf]
    10. Schrader M, Schulz-Knappe P. Peptidomics technologies for human body fluids . Trends Biotechnol. 2001:19:S55-S60 [PubMed][pdf]
    11. Weir M. et al. Insights into protein function through large-scale computational analysis of sequence and structure. Trends Biotechnol. 2001:19:S61-S66 [PubMed][pdf]
    12. Jhoti H. High-throughput structural proteomics using x-rays . Trends Biotechnol. 2001:19:S67-S71 [PubMed][pdf]

2-d gel electrophoresis and mass spectroscopy applications in expression profiling

  1. Seow TK, Korke R, Liang RC, Ong SE, Ou K, Wong K, Hu WS, Chung MC. Proteomic Investigation of Metabolic Shift in Mammalian Cell Culture. Biotechnol Prog. 2001 Dec 7;17(6):1137-1144. [PubMed]
  2. Griffin TJ, Aebersold R. Advances in proteome analysis by mass spectrometry.  J Biol Chem. 2001 Dec 7; 276:45497-45500  [PubMed]
  3. Griffin TJ et al. Advances in proteome analysis by mass spectrometry. Current Opinion in Biotechnol. 2001 Dec; 12:607-612. [PubMed]
  4. Clarke NJ, Crow FW, Younkin S, Naylor S. Analysis of in vivo-derived amyloid-beta polypeptides by on-line two-dimensional chromatography-mass spectrometry . Anal Biochem. 2001 Nov 1;298(1):32-9. [PubMed]
  5. Schonberger SJ, Edgar PF, Kydd R, Faull RL, Cooper GJ. Proteomic analysis of the brain in Alzheimer's disease: Molecular phenotype of a complex disease process. Proteomics. 2001 Nov;1(12):1519-1528. [PubMed]
  6. Skylas DJ, Copeland L, Rathmell WG, Wrigley CW. The wheat-grain proteome as a basis for more efficient cultivar identification. Proteomics. 2001 Nov;1(12):1542-1546. [PubMed]
  7. Ong S E, Pandey A B. An evaluation of the use of two-dimensional gel electrophoresis in proteomics. Biomol Eng. 2001 Nov;18(5):195-205. [PubMed]
  8. Mills GB, Bast RC Jr, Srivastava S.  Future for ovarian cancer screening: novel markers from emerging technologies of transcriptional profiling and proteomics.   J Natl Cancer Inst. 2001 Oct 3;93(19):1437-9. [PubMed]
  9. Demirev PA, Lin JS, Pineda FJ, Fenselaut C. Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search  algorithms for characterization of intact H. pylori.  Anal Chem. 2001 Oct 1;73(19):4566-73. [PubMed]
  10. Issaq HJ. The role of separation science in proteomics research.  Electrophoresis. 2001 Oct;22(17):3629-38. [PubMed]
  11. Wulfkuhle JD, McLean KC, Paweletz CP, Sgroi DC, Trock BJ, Steeg PS, Petricoin EF 3rd. New approaches to proteomic analysis of breast cancer. Proteomics. 2001 Oct;1(10):1205-15. [PubMed]
  12. Hondermarck H, Vercoutter-Edouart AS, Revillion F, Lemoine J, el-Yazidi-Belkoura I, Nurcombe V, Peyrat JP. Proteomics of breast cancer for marker discovery and signal pathway profiling. Proteomics. 2001 Oct;1(10):1216-32. [PubMed]
  13. Ragno S, Romano M, Howell S, Pappin DJ, Jenner PJ, Colston MJ. Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: a combined transcriptomic and proteomic approach.  Immunology. 2001 Sep;104(1):99-108. [PubMed]
  14. von Eggeling F, Junker K, Fiedle W, Wollscheid V, Durst M, Claussen U, Ernst G.  Mass spectrometry meets chip technology: a new proteomic tool in cancer research?  Electrophoresis. 2001 Aug;22(14):2898-902. [PubMed]
  15. Doucette A, Li L. Investigation of the applicability of a sequential digestion protocol using trypsin and leucine aminopeptidase M for protein identification by matrix-assisted laser desorption/ionization--time of flight mass spectrometry.  Proteomics. 2001 Aug;1(8):987-1000. [PubMed]

    16. Belghazi M, Bathany K, Hountondji C, Grandier-Vazeille X, Manon S, Schmitter JM. Analysis of protein sequences and protein complexes by matrix-assisted laser desorption/ionization mass spectrometry.  Proteomics. 2001 Aug;1(8):946-54. [PubMed]
  16. Derrick PJ, Patterson SD. Mass spectrometry of proteomics. Proteomics. 2001 Aug;1(8):925-6. [PubMed]
  17. Lay JO Jr. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom Rev. 2001 Jul-Aug;20(4):172-94. [PubMed]
  18. Shen Y, Tolic N, Zhao R, Pasa-Tolic L, Li L, Berger SJ, Harkewicz R, Anderson GA, Belov ME, Smith RD. High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry. Anal Chem. 2001 Jul 1;73(13):3011-21. [PubMed]
  19. Hoffmann P, Ji H, Moritz RL, Connolly LM, Frecklington DF, Layton MJ, Eddes JS, Simpson RJ.  Continuous free-flow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM 1215: a non two-dimensional gel electrophoresis-based proteome analysis strategy. Proteomics. 2001 Jul;1(7):807-18. [PubMed]
  20. Lim D, Hains P, Walsh B, Bergquist P, Nevalainen H. Proteins associated with the cell envelope of Trichoderma reesei: a proteomic approach.  Proteomics. 2001 Jul;1(7):899-909. [PubMed]
  21. Premstaller A, Oberacher H, Walcher W, Timperio AM, Zolla L, Chervet JP, Cavusoglu N, van Dorsselaer A, Huber CG. High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies.  Anal Chem. 2001 Jun 1;73(11):2390-6. [PubMed]
  22. Guillonneau F, Guieysse AL, Le Caer JP, Rossier J, Praseuth D. Selection and identification of proteins bound to DNA triple helical structures by combination of 2D electrophoresis and MALDI-TOF mass spectrometry. Nucleic Acid Res 2001. Jun 1; 29: 2427-2436. [PubMed]
  23. Kennedy S. Proteomic profiling from human samples: the body fluid alternative. Toxicol Lett. 2001 Mar 31;120(1-3):379-84. [PubMed]
  24. Smith RD, Pasa-Tolic L, Lipton MS, Jensen PK, Anderson GA, Shen Y, Conrads TP, Udseth HR, Harkewicz R, Belov ME, Masselon C, Veenstra TD. Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry. Electrophoresis. 2001 May;22(9):1652-68. [PubMed]
  25. Hamdan M, Bordini E, Galvani M, Righetti PG. Protein alkylation by acrylamide, its N-substituted derivatives and cross-linkers and its relevance to proteomics: a matrix assisted laser desorption/ionization-time of flight-mass spectrometry study.  Electrophoresis. 2001 May;22(9):1633-44. [PubMed]
  26. Moller A, Soldan M, Volker U, Maser E.  Two-dimensional gel electrophoresis: a powerful method to elucidate cellular responses to toxic  compounds. Toxicology. 2001 Mar 7;160(1-3):129-138. [PubMed]
  27. Westergren-Thorsson G, Malmstrom J, Marko-Varga G.  Proteomics - the protein expression technology to study connective tissue biology .  J Pharm Biomed Anal. 2001 Mar;24(5-6):815-824. [PubMed]
  28. Koc EC, Burkhart W, Blackburn K, Koc H, Moseley A, Spremulli LL. Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach.  Protein Sci. 2001 Mar;10(3):471-481. [PubMed]
  29. Davidsson P, Paulson L, Hesse C, Blennow K, Nilsson CL. Proteome studies of human cerebrospinal fluid and brain tissue using a preparative two-dimensional electophoresis approach prior to mass spectrometry. Proteomics. 2001 Mar;1(3):444-52. [PubMed]
  30. Bell AW, Ward MA, Freeman HN, Choudhary JS, Blackstock WP, Lewis AP, Fazel A, Gushue JN, Paiement J, Palcy S,  Chevet E, Lafreniere-Roula M, Solari R, Thomas DY, Rowley A, Bergeron JM. Proteomics characterization of abundant Golgi membrane proteins. J Biol Chem. 2001 Feb 16; 276(7):5152-5165. [PubMed]
  31. Yoshida Ki K, Kobayashi K, Miwa Y, Kang CM, Matsunaga M, Yamaguchi H, Tojo S, Yamamoto M, Nishi R, Ogasawara N, Nakayama T, Fujita Y.  Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res. 2001 Feb 1;29(3):683-692. [PubMed]
  32. Fey SJ, Larsen PM.  2D or not 2D.  Curr Opin Chem Biol. 2001 Feb 1;5(1):26-33. [PubMed]
  33. Harvey DJ. Identification of protein-bound carbohydrates by mass spectrometry.  Proteomics. 2001 Feb;1(2):311-28. [PubMed]
  34. Aebersold R, Goodlett DR. Mass spectrometry in proteomics.  Chem Rev. 2001 Feb;101(2):269-95. [PubMed]
  35. Bichsel VE, Liotta LA, Petricoin EF 3rd.   Cancer proteomics: from biomarker discovery to signal pathway profiling.  Cancer J. 2001 Jan-Feb;7(1):69-78. [PubMed]
  36. Verhaert P, Uttenweiler-Joseph S, de Vries M, Loboda A, Ens W, Standing KG. Matrix-assisted laser desorption/ionization quadrupole time-of-flight mass spectrometry: an elegant tool for peptidomics. Proteomics. 2001 Jan;1(1):118-31. [PubMed]
  37. Spahr CS, Davis MT, McGinley MD, Robinson JH, Bures EJ, Beierle J, Mort J, Courchesne PL, Chen K, Wahl RC, Yu W, Luethy R, Patterson SD. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry I. Profiling an unfractionated tryptic digest. Proteomics 2001. Jan; 1:93-107 [PubMed]
  38. Davis MT, Spahr CS, McGinley MD, Robinson JH, Bures EJ, Beierle J, Mort J, Yu W, Luethy R, Patterson SD. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry II. Limitations of complex mixture analyses. Proteomics 2001. Jan; 1:108-117 [PubMed]
  39. Butt A, Davison MD, Smith GJ, Young JA, Gaskell SJ, Oliver SG, Beynon RJ. Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis. Proteomics. 2001 Jan;1(1):42-53. [PubMed]
  40. Voss T, Ahorn H, Haberl P, Dohner H, Wilgenbus K. Correlation of clinical data with proteomics profiles in 24 patients with B-cell chronic lymphocyticleukemia. Int. J. Cancer. 2001; 91:180-186. [PubMed]
  41. Mann M, Hendrickson RC, Pandey A. ANALYSIS OF PROTEINS AND PROTEOMES BY MASS SPECTROMETRY. Annu Rev Biochem. 2001;70:437-473. [PubMed]
  42. Cheon MS, Fountoulakis M, Dierssen M, Ferreres JC, Lubec G. Expression profiles of proteins in fetal brain with Down syndrome. J Neural Transm Suppl. 2001;(61):311-9. [PubMed]

Protein-protein interaction

  1. Hernandez H, Robinson CV. Dynamic Protein Complexes: Insights from Mass Spectrometry. J Biol Chem. 2001 Dec 14;276(50):46685-46688. [PubMed]
  2. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein-Protein Interactions or “Interologs". Genome Res. 2001 Dec; 11:2120-2126. [PubMed]
  3. Wollacott AM, Desjarlais JR. Virtual interaction profiles of proteins.J Mol Biol. 2001 Oct 19;313(2):317-42. [PubMed]
  4. Ashman K, Moran MF, Sicheri F, Pawson T, Tyers M. Cell Signalling - The Proteomics of It All.  Sci STKE. 2001 Oct 9;2001(103):PE33. [PubMed]
  5. Davy A, Bello P, Thierry-Mieg N, Vaglio P, Hitti J, Doucette-Stamm L, Thierry-Mieg D, Reboul J, Boulton S, Walhout AJ, Coux O, Vidal M. A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep. 2001 Sep;2(9):821-828. [PubMed]
  6. Pazos F, Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 2001 Sep;14(9):609-14. [PubMed]
  7. Pelletier J, Sidhu S. Mapping protein–protein interactions with combinatorial biology methods. Curr Opin Biotechnol. 2001 Aug; 12:340-347. [PubMed]
  8. Walhout AJ, Vidal M.  High-throughput yeast two-hybrid assays for large-scale protein interaction mapping.  Methods. 2001 Jul;24(3):297-306. [PubMed]
  9. Figeys D, McBroom LD, Moran MF.  Mass spectrometry for the study of protein-protein interactions. Methods. 2001 Jul;24(3):230-9. [PubMed]
  10. Mrowka R. A Java applet for visualizing protein-protein interaction. Bioinformatics. 2001 Jul;17(7):669-71. [PubMed]
  11. Tasara T, Hottiger MO, Hubscher U. Functional genomics in HIV-1 virus replication: protein-protein interactions as a basis for recruiting the host cell machinery for viral propagation. Biol Chem. 2001 Jul;382(7):993-9. [PubMed]
  12. Legrain P, Wojcik J, Gauthier J. Protein-protein interaction maps: a lead towards cellular functions. Trends Genet. 2001 Jun;17(6):346-52. [PubMed]
  13. Wojcik J, Schachter V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics. 2001 Jun;17 Suppl 1:S296-305. [PubMed]
  14. Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature. 2001 May 3;411(6833):41-2. [PubMed]
  15. Hasty J, Collins JJ. Protein interactions Unspinning the web. Nature. 2001 May 3;411(6833):30-31. [PubMed]
  16. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y.  A comprehensive two-hybrid analysis to explore the yeast protein interactome.    Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-4574. [PubMed][pdf]
  17.  Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast. 2001 Apr;18(6):523-531. [PubMed]
  18. Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM.  Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues. Nat Med. 2001 Apr;7(4):493-496. [PubMed]
  19. Marcotte EM, Xenarios I, Eisenberg D.  Mining literature for protein-protein interactions.  Bioinformatics. 2001 Apr;17(4):359-363. [PubMed]
  20. Jacq B. Protein function from the perspective of molecular interactions and genetic networks. Brief Bioinform. 2001 Mar;2(1):38-50. [PubMed]
  21. Boulton SJ, Vincent S, Vidal M.  Use of protein-interaction maps to formulate biological questions.  Curr Opin Chem Biol. 2001 Feb 1;5(1):57-62. [PubMed]
  22. Rain J, Selig L, de Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, Chemama Y, Labigne A, Legrain P. The protein-protein interaction map of helicobacter pylori. Nature 2001 Jan 11; 409: 211-215 [pdf]
  23. Walhout AJ, Vidal M. Protein interaction maps for model organisms. Nat Rev Mol Cell Biol. 2001 Jan;2(1):55-62. Review. [PubMed]
  24. Joung JK. Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system. J Cell Biochem. 2001 84: S37:53-57 [PubMed]

Application

  1. Van Eyk JE.  Proteomics: unraveling the complexity of heart disease and striving to change cardiology. Curr Opin Mol Ther. 2001 Dec;3(6):546-53. [PubMed]
  2. Hanash SM.  Global profiling of gene expression in cancer using genomics and proteomics. Curr Opin Mol Ther. 2001 Dec;3(6):538-45. [PubMed]
  3. Hippler M, Klein J, Fink A, Allinger T, Hoerth P. Towards functional proteomics of membrane protein complexes: analysis of thylakoid membranes from Chlamydomonas reinhardtii. Plant J. 2001 Dec;28(5):595-606. [PubMed]
  4. Liotta LA, Kohn EC, Petricoin EF. Clinical Proteomics: Personalized Molecular Medicine. JAMA. 2001 Nov 14;286(18):2211-2214. [PubMed]
  5. Kobayashi R. A Proteomics Approach to Find a New Breast Cancer-specific Antigenic Marker: Commentary re: Protemics-based Identification of RS/DJ-1 as a Novel Circulating Tumor Antigen in Breast Cancer. Clin. Cancer Res., 7: 3328-3335, 2001. Clin Cancer Res. 2001 Nov;7(11):3325-7. [PubMed]
  6. Brichory F, Beer D, LeNaour F, Giordano T, Hanash S. Proteomics-based Identification of Protein Gene Product 9.5 as a Tumor Antigen That Induces a Humoral Immune Response in Lung Cancer.  Cancer Res. 2001 Nov 1;61(21):7908-12. [PubMed]
  7. Grant SG, Blackstock WP. Proteomics in neuroscience: from protein to network.  J Neurosci. 2001 Nov 1;21(21):8315-8. [PubMed]
  8. Owens J. Topological proteomics: a new approach to drug discovery.   Drug Discov Today. 2001 Nov 1;6(21):1081-1082. [PubMed]
  9. Le Naour F, Misek DE, Krause MC, Deneux L, Giordano TJ, Scholl S, Hanash SM.  Proteomics-based Identification of RS/DJ-1 as a Novel Circulating Tumor Antigen in Breast Cancer.  Clin Cancer Res. 2001 Nov;7(11):3328-35. [PubMed]
  10. Poon TC, Johnson PJ. Proteome analysis and its impact on the discovery of serological tumor markers.  Clin Chim Acta. 2001 Nov;313(1-2):231-9. [PubMed]
  11. Martin DB, Nelson PS. From genomics to proteomics: techniques and applications in cancer research. Trends Cell Biol. 2001 Nov;11(11):S60-5. [PubMed]
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  46. Klade CS, Voss T, Krystek E, Ahorn H, Zatloukal K, Pummer K, Adolf GR. Identification of tumor antigens in renal cell carcinoma by serological proteome analysis. Proteomics. 2001 Jul;1(7):890-8. [PubMed]
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Structural genomics

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  7. Van Regenmortel MH. Proteomics versus genomics. What type of structure-function relationship are we looking for? J Mol Recognit. 2001 Nov;14(6):321-2. [PubMed]
  8. Lian LY. et al. Labelling approaches for protein structural studies by solution-state and solid-state NMR. Prog Nucl Mag Reson Spec. 2001 Oct 19; 39:171-190. [PubMed]
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  15. Brenner SE. A tour of structural genomics.  Nat Rev Genet. 2001 Oct;2(10):801-9. [PubMed]
  16. Romijn JA, Smit JW. Structural genomics in endocrinology. Pharmacogenomics. 2001 Nov;2(4):353-60. [PubMed]
  17. Heinemann U, Illing G, Oschkinat H. High-throughput three-dimensional protein structure determination. Curr Opin Biotechnol. 2001 Aug; 12:348-354. [PubMed]
  18. Gedeck P, Willett P.  Visual and computational analysis of structure-activity relationships in high-throughput screening data.  Curr Opin Chem Biol. 2001 Aug;5(4):389-95. [PubMed]
  19. Mittl PR, Grutter MG. Structural genomics: opportunities and challenges [Review] Curr Opin Chem Biol. 2001 August; 5: 402-408. [PubMed]
  20. Sawyer TK. Proteomics--structure and function. Biotechniques. 2001 Jul;31(1):156-8, 160. [PubMed]
  21. Teichmann SA, Murzin AG, Chothia C. Determination of protein function, evolution and interactions by structural genomics.  Curr Opin Struct Biol. 2001 Jun;11(3):354-63. [PubMed]
  22. Bonneau R, Tsai J, Ruczinski I, Baker D. Functional Inferences from Blind ab Initio Protein Structure Predictions. J Stru Biol. 2001 May; 134:186-190 [PubMed]
  23. Pokala N, Handel TM.  Review: protein design-where we were, where we are, where we're going.  J Struct Biol. 2001 May;134(2-3):269-81. [PubMed]
  24. Clarke TE, Tari LW, Vogel HJ. Structural biology of bacterial iron uptake systems. Curr Top Med Chem. 2001 May;1(1):7-30. [PubMed]
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Technical issues

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  5. Cramer R, Corless S. The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics.  Rapid Commun Mass Spectrom. 2001 Nov 30;15(22):2058-2066. [PubMed]
  6. Stevens FJ.  Caveat receptor: proteomes on display.  Comb Chem High Throughput Screen. 2001 Nov;4(7):599-602. [PubMed]
  7. Georgiou HM, Rice GE, Baker MS. Proteomic analysis of human plasma: Failure of centrifugal ultrafiltration to remove albumin and other high molecular weight proteins. Proteomics. 2001 Nov;1(12):1503-1506. [PubMed]
  8. Zhang R, Sioma CS, Wang S, Regnier FE. Fractionation of isotopically labeled peptides in quantitative proteomics. Anal Chem. 2001 Nov 1;73(21):5142-9. [PubMed]
  9. Meri S, Baumann M. Proteomics: posttranslational modifications, immune responses and current analytical tools. Biomol Eng. 2001 Nov;18(5):213-20. [PubMed]
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  13. Hanash S. Mining the cancer proteome. Proteomics. 2001 Oct;1(10):1189-90. [PubMed]
  14. Craven RA, Banks RE. Laser capture microdissection and proteomics: possibilities and limitation. Proteomics. 2001 Oct;1(10):1200-4. [PubMed]
  15. Randic M, Zupan J, Novic M. On 3-d graphical representation of proteomics maps and their numerical characterization. J Chem Inf Comput Sci. 2001 Sep-Oct;41(5):1339-44. [PubMed]
  16. Randic M. On graphical and numerical characterization of proteomics maps. J Chem Inf Comput Sci. 2001 Sep-Oct;41(5):1330-8. [PubMed]
  17. Ziegler Z. Virtual 2-D proteomics. Anal Chem. 2001 Sep 1;73(17):473A [PubMed]
  18. Doi N, Yanagawa H. Genotype-phenotype linkage for directed evolution and screening of combinatorial protein libraries.  Comb Chem High Throughput Screen. 2001 Sep;4(6):497-509. [PubMed]
  19. Lindl K, Kresse M, Muller RH. Evaluation of desorption of proteins adsorbed to hydrophilic surfaces by two-dimensional electrophoresis. Proteomics. 2001 Sep;1(9):1059-66. [PubMed]
  20. Patricelli MP, Giang DK, Stamp LM, Burbaum JJ. Direct visualization of serine hydrolase activities in complex proteomes using fluorescent active site-directed probes. Proteomics. 2001 Sep;1(9):1067-71. [PubMed]
  21. Ericsson D, Ekstrom S, Nilsson J, Bergquist J, Marko-Varga G, Laurell T. Downsizing proteolytic digestion and analysis using dispenser-aided sample handling and nanovial matrix-assisted laser/desorption ionization-target arrays. Proteomics. 2001 Sep;1(9):1072-81. [PubMed]
  22. Miliotis T, Marko-Varga G, Nilsson J, Laurell T. Development of silicon microstructures and thin-film MALDI target plates for automated proteomics sample identifications.  J Neurosci Methods. 2001 Aug 15;109(1):41-6. [PubMed]
  23. Hakansson K, Emmett MR, Hendrickson CL, Marshall AG. High-sensitivity electron capture dissociation tandem FTICR mass spectrometry of microelectrosprayed peptides.  Anal Chem. 2001 Aug 1;73(15):3605-10. [PubMed]
  24. Lawrie LC, Curran S, McLeod HL, Fothergill JE, Murray GI. Application of laser capture microdissection and proteomics in colon cancer. Mol Pathol. 2001 Aug;54(4):253-8. [PubMed]
  25. von Eggeling F, Junker K, Fiedle W, Wollscheid V, Durst M, Claussen U, Ernst G.  Mass spectrometry meets chip technology: a new proteomic tool in cancer research?  Electrophoresis. 2001 Aug;22(14):2898-902. [PubMed]

    26. Li J, Tremblay TL, Wang C, Attiya S, Harrison DJ, Thibault P. Integrated system for high-throughput protein identification using a microfabricated device coupled to capillary electrophoresis/nanoelectrospray mass spectrometry.   Proteomics. 2001 Aug;1(8):975-86. [PubMed]
  26. Stensballe A, Jensen ON.  Simplified sample preparation method for protein identification by matrix-assisted laser desorption/ionization mass spectrometry: in-gel digestion on  the probe surface. Proteomics. 2001 Aug;1(8):955-66. [PubMed]
  27. Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AA, Babbitt PC. Functional assignment of the 20S proteasome from T. Brucei using mass spectrometry and new bioinformatics approaches.  J Biol Chem. 2001 Jul 27; 276: 28327-28339 [PubMed]
  28. Wang S, Regnier FE. Proteomics based on selecting and quantifying cysteine containing peptides by covalent chromatography.  J Chromatogr A. 2001 Jul 27;924(1-2):345-57. [PubMed]
  29. Jiang Y, Lee CS. On-line coupling of micro-enzyme reactor with micro-membrane chromatography for protein digestion, peptide separation, and protein identification using electrospray ionization mass spectrometry.   J Chromatogr A. 2001 Jul 27;924(1-2):315-22. [PubMed]
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  33. Lesley SA. High-Throughput Proteomics: Protein Expression and Purification in the Postgenomic World. Protein Expr Purif. 2001 Jul;22(2):159-164. [PubMed]
  34. Lanne B, Potthast F, Hoglund A, Brockenhuus von Lowenhielm H, Nystrom AC, Nilsson F, Dahllof B. Thiourea enhances mapping of the proteome from murine white adipose tissue.  Proteomics. 2001 Jul;1(7):819-28. [PubMed]
  35. Conrad CC, Choi J, Malakowsky CA, Talent JM, Dai R, Marshall P, Gracy RW. Identification of protein carbonyls after two-dimensional electrophoresis. Proteomics. 2001 Jul;1(7):829-34. [PubMed]
  36. Sinha P, Poland J, Schnolzer M, Rabilloud T. A new silver staining apparatus and procedure for matrix-assisted laser desorption/ionization-time of flight analysis of proteins after two-dimensional electrophoresis.   Proteomics. 2001 Jul;1(7):835-40. [PubMed]
  37. Steinberg TH, Pretty On Top K, Berggren KN, Kemper C, Jones L, Diwu Z, Haugland RP, Patton WF.  Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots.  Proteomics. 2001 Jul;1(7):841-55. [PubMed]
  38. Veeser S, Dunn MJ, Yang GZ. Multiresolution image registration for two-dimensional gel electrophoresis. Proteomics. 2001 Jul;1(7):856-70. [PubMed]
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  42. Nakai K. Prediction of in Vivo Fates of Proteins in the Era of Genomics and Proteomics. J Stru Biol. 2001 May; 134:103-116 [PubMed]
  43. Zhou X, Gonnet G, Hallett M, Munchbach M, Folkers G, James P. Cell fingerprinting: an approach to classifying cells according to mass profiles of digests of protein extracts.  Proteomics. 2001 May;1(5):683-90. [PubMed]
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  46. Dwek MV, Ross HA, Leathem AJ. Proteome and glycosylation mapping identifies post-translational modifications associated with aggressive breast cancer. Proteomics. 2001 Jun;1(6):756-62. [PubMed]
  47. Wang S, Regnier FE. Proteolysis of whole cell extracts with immobilized enzyme columns as part of multidimensional chromatography.  J Chromatogr A. 2001 Apr 13;913(1-2):429-36. [PubMed]
  48. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y.  A comprehensive two-hybrid analysis to explore the yeast protein interactome.    Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-4574. [PubMed][pdf]
  49. Ahn NG, Resing KA.  Toward the phosphoproteome. Nat Biotechnol. 2001 Apr;19(4):317-318. [PubMed]
  50. Zhou H, Watts JD, Aebersold R.  A systematic approach to the analysis of protein phosphorylation.  Nat Biotechnol. 2001 Apr;19(4):375-378. [PubMed]
  51. Oda Y, Nagasu T, Chait BT.  Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol. 2001 Apr;19(4):379-382. [PubMed]
  52. Pradet-Balade B. et. al. Translation control: bridging the gap between genomics and proteomics? Trends Biochem Sci. 2001. Apr; 26:225-229. [PubMed]
  53. Paweletz CP, Liotta LA, Petricoin EF. New technologies for biomarker analysis of prostate cancer progression: Laser capture microdissection and tissue proteomics.  Urology. 2001 Apr;57(4 Suppl 1):160-163. [PubMed]
  54. Shen Y, Zhao R, Belov ME, Conrads TP, Anderson GA, Tang K, Pasa-Tolic L, Veenstra TD, Lipton MS, Udseth HR, Smith RD.  Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass  spectrometry for proteomics.  Anal Chem. 2001 Apr 15;73(8):1766-75. [PubMed]
  55. Washburn MP, Wolters D, Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001. Mar; 19:242-247 [PubMed]
  56. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics. 2001 Mar;1(3):377-96 [PubMed]
  57. Westbrook JA, Yan JX, Wait R, Dunn MJ. A combined radiolabelling and silver staining technique for improved visualisation, localisation, and identification of proteins separated by two-dimensional gel electrophoresis.   Proteomics. 2001 Mar;1(3):370-6. [PubMed]
  58. Fisch I.  Peptide Display in Functional Genomics.  Comb Chem High Throughput Screen. 2001 Feb 1;4(1):157-169. [PubMed]
  59. Schulz-Knappe P, Zucht HD, Heine G, Jurgens M, Hess R, Schrader M. Peptidomics: The Comprehensive Analysis of Peptides in Complex Biological Mixtures. Comb Chem High Throughput Screen. 2001 Feb 1;4(1):207-217. [PubMed]
  60. Brancia FL, Butt A, Beynon RJ, Hubbard SJ, Gaskell SJ, Oliver SG. A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics.  Electrophoresis. 2001 Feb;22(3):552-9. [PubMed]
  61. Larsen MR, Sorensen GL, Fey SJ, Larsen PM, Roepstorff P. Phospho-proteomics: evaluation of the use of enzymatic de-phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis. Proteomics. 2001 Feb;1(2):223-38. [PubMed]
  62. Sickmann A, Meyer HE. Phosphoamino acid analysis. Proteomics. 2001 Feb;1(2):200-6. [PubMed]
  63. Butt A, Davison MD, Smith GJ, Young JA, Gaskell SJ, Oliver SG, Beynon RJ. Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis. Proteomics. 2001 Jan;1(1):42-53. [PubMed]
  64. Larsen MR, Sorensen GL, Fey SJ, Larsen PM, Roepstorff P.  Phospho-proteomics: evaluation of the use of enzymatic de-phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis. Electrophoresis. 2001;22(4):223-38. [PubMed]
  65. Rudd PM, Colominas C, Royle L, Murphy N, Hart E, Merry AH, Hebestreit HF, Dwek RA. A high-performance liquid chromatography based strategy for rapid, sensitive sequencing of N-linked oligosaccharide modifications to proteins in sodium dodecyl sulphate polyacrylamide electrophoresis gel bands. Electrophoresis. 2001;22(4):285-94. [PubMed]
  66. Katayama H, Nagasu T, Oda Y. Improvement of in-gel digestion protocol for peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 2001;15(16):1416-21. [PubMed]
  67. Ma D, Li M. Applications of display technologies to proteomic analyses. J Cell Biochem. 2001 84: S37:34-41 [PubMed]

Software

  1. Vihinen M. Bioinformatics in proteomics. Biomol Eng. 2001 Nov;18(5):241-8. [PubMed]
  2. Cooper CA, Gasteiger E, Packer NH. GlycoMod--a software tool for determining glycosylation compositions from mass spectrometric data.  Proteomics. 2001 Feb;1(2):340-9. [PubMed]
  3. Sem DS, Yu L, Coutts SM, Jack R. Object?oriented approach to drug design enabled by NMR SOLVE: First real?time structural tool for characterizing protein?ligand interactions. J Cell Biochem. 2001;84(S37):99-105. [PubMed]

Database

  1. Nyman TA, Rosengren A, Syyrakki S, Pellinen TP, Rautajoki K, Lahesmaa R. A proteome database of human primary T helper cells. Electrophoresis. 2001 Dec;22(20):4375-82. [PubMed]
  2. Weiller GF, Djordjevic MJ, Caraux G, Chen H, Weinman JJ. A specialised proteomic database for comparing matrix-assisted laser desorption/ionization-time of flight mass spectrometry data of tryptic peptides with corresponding sequence database segments. Proteomics. 2001 Nov;1(12):1489-1494. [PubMed]
  3. Oh JM, Brichory F, Puravs E, Kuick R, Wood C, Rouillard JM, Tra J, Kardia S, Beer D, Hanash S. A database of protein expression in lung cancer. Proteomics. 2001 Oct;1(10):1303-19. [PubMed]
  4. Wojcik J, Schachter V. Proteomic databases and software on the web.   Brief Bioinform. 2000 Sep;1(3):250-9. [PubMed]
  5. Xenarios I, Eisenberg D.  Protein interaction databases. Curr Opin Biotechnol. 2001 Aug; 12:334-339 [PubMed]
  6. Jung E, Veuthey AL, Gasteiger E, Bairoch A. Annotation of glycoproteins in the SWISS-PROT database. Proteomics. 2001 Feb;1(2):262-8. [PubMed]
  7. Baxevanis AD.The molecular biology database collection: an updated compilation of biological database resources.  Nucleic Acids Res. 2001 Jan 1;29(1):1-10.  [PubMed]
  8. Wu C. Protein information resource: a community resource for expert annotation of protein data. Nucleic Acids Res. 2001 Jan 1;29(1):29-32. [PubMed]
  9. Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D.  DIP: the database of interacting proteins: 2001 update. Nucleic Acids Res. 2001 Jan 1;29(1):239-41. [PubMed]
  10. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. BIND-The biomolecular interaction network database. Nucleic Acids Res. 2001 Jan 1;29(1):242-5. [PubMed]
  11. Sanchez JC, Chiappe D, Converset V, Hoogland C, Binz PA, Paesano S, Appel RD, Wang S, Sennitt M, Nolan A, Cawthorne MA, Hochstrasser DF. The mouse SWISS-2D PAGE database: a tool for proteomics study of diabetes and obesity.  Proteomics. 2001 Jan;1(1):136-63. [PubMed]
last updated: 25 Aug 2002
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