My proteomics journal watch - year 2004 Jan-Jun [ 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. Garber K. Debate rages over proteomic patterns. J Natl Cancer Inst. 2004 Jun 2;96(11):816-8. [PubMed]
  2. Hanash S. Building a foundation for the human proteome: the role of the Human Proteome Organization. J Proteome Res. 2004 Mar-Apr;3(2):197-9. [PubMed]
  3. Jia H, Louet S. China pushes liver proteomics. Nat Biotechnol. 2004 Feb;22(2):136.  [PubMed]
  4. Werner T. Proteomics and regulomics: The yin and yang of functional genomics. Mass Spectrom Rev. 2004 Feb;23(1):25-33. [PubMed]
  5. Hanash S. HUPO initiatives relevant to clinical proteomics. Mol Cell Proteomics. 2004 Jan 27 [Epub ahead of print] [PubMed]
  6. Powell MJ, Timperman AT. Proteome analysis. Methods Mol Biol. 2004;251:387-400. [PubMed]

Application

  1. Wilson KE, Ryan MM, Prime JE, Pashby DP, Orange PR, O'Beirne G, Whateley JG, Bahn S, Morris CM. Functional genomics and proteomics: application in neurosciences. J Neurol Neurosurg Psychiatry. 2004 Apr;75(4):529-538. [PubMed]
  2. Davis TN. Protein localization in proteomics. Curr Opin Chem Biol.  2004 Feb [PubMed]
  3. Navas A, Albar JP. Application of proteomics in phylogenetic and evolutionary studies. Proteomics. 2004 Feb;4(2):299-302. [PubMed]
  4. Canovas FM, Dumas-Gaudot E, Recorbet G, Jorrin J, Mock HP, Rossignol M. Plant proteome analysis. Proteomics. 2004 Feb;4(2):285-98. [PubMed]
  5. Martinez I, Jakobsen Friis T. Application of proteome analysis to seafood authentication. Proteomics. 2004 Feb;4(2):347-54. [PubMed]
  6. Barnes S, Kim H. Nutriproteomics: identifying the molecular targets of nutritive and non-nutritive components of the diet. J Biochem Mol Biol. 2004 Jan 31;37(1):59-74. [PubMed]
  7. Park OK. Proteomic studies in plants. J Biochem Mol Biol. 2004 Jan 31;37(1):133-8. [PubMed]
  8. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan; 4(1): 59-77. [PubMed]
  9. McNulty DE, Slemmon JR. Peptide proteomics. Methods Mol Biol. 2004;244:411-24. [PubMed]

Basic Science Studies

  1. Archambault V, Chang EJ, Drapkin BJ, Cross FR, Chait BT, Rout MP. Targeted proteomic study of the cyclin-cdk module. Mol Cell. 2004 Jun 18;14(6):699-711. [PubMed]
  2. Knight CG, Kassen R, Hebestreit H, Rainey PB. From The Cover: Global analysis of predicted proteomes: Functional adaptation of physical properties. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8390-5. [PubMed]
  3. Brocchieri L. Environmental signatures in proteome properties. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8257-8.[PubMed]
  4. Sam-Yellowe TY, Florens L, Johnson JR, Wang T, Drazba JA, Le Roch KG, Zhou Y, Batalov S, Carucci DJ, Winzeler EA, Yates JR 3rd. A Plasmodium Gene Family Encoding Maurer's Cleft Membrane Proteins: Structural Properties and Expression Profiling. Genome Res. 2004 Jun;14(6):1052-9. [PubMed]
  5. Wollscheid B, Watts JD, Aebersold R. Proteomics/genomics and signaling in lymphocytes. Curr Opin Immunol. 2004 Jun;16(3):337-44. [PubMed]
  6. Wang D, Jensen R, Gendeh G, Williams K, Pallavicini MG. Proteome and transcriptome analysis of retinoic acid-induced differentiation of human acute promyelocytic leukemia cells, NB4. J Proteome Res. 2004 May-Jun;3(3):627-35. [PubMed]
  7. Choudhary J, Grant SG. Proteomics in postgenomic neuroscience: the end of the beginning. Nat Neurosci. 2004 May;7(5):440-5. [PubMed]
  8. Ruse CI, Tan FL, Kinter M, Bond M. Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome. Proteomics. 2004 May;4(5):1505-16. [PubMed]
  9. Moore JM, Galicia SJ, McReynolds AC, Nguyen NH, Scanlan TS, Guy RK. Quantitative proteomics of the thyroid hormone receptor coregulator interactions. J Biol Chem. 2004 Apr 19 [Epub ahead of print] [PubMed]
  10. Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, Kawamura Y, Mitsui T, Mikami S, Tozawa Y, Yoshinaga T, Komatsu S. Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments. Mol Genet Genomics. 2004 Apr 7 [Epub ahead of print] [PubMed]
  11. Johnson MD, Yu LR, Conrads TP, Kinoshita Y, Uo T, Matthews JD, Lee SW, Smith RD, Veenstra TD, Morrison RS. Proteome analysis of DNA damage-induced neuronal death using high throughput mass spectrometry. J Biol Chem. 2004 Apr 1 [Epub ahead of print] [PubMed]
  12. Godl K, Daub H. Proteomic Analysis of Kinase Inhibitor Selectivity and Function. Cell Cycle. 2004 Apr [Epub ahead of print] [PubMed]
  13. Vitorino R, Lobo MJ, Ferrer-Correira AJ, Dubin JR, Tomer KB, Domingues PM, Amado FM. Identification of human whole saliva protein components using proteomics. Proteomics. 2004 Apr;4(4):1109-15. [PubMed]
  14. Daub H, Godl K, Brehmer D, Klebl B, Muller G. Evaluation of kinase inhibitor selectivity by chemical proteomics. Assay Drug Dev Technol. 2004 Apr;2(2):215-24. [PubMed]
  15. Glickman JF, Auld D. The proteomics of kinase selectivity. Assay Drug Dev Technol. 2004 Apr;2(2):237-8. [PubMed]
  16. Taylor CM, Marta CB, Claycomb RJ, Han DK, Rasband MN, Coetzee T, Pfeiffer SE. Proteomic mapping provides powerful insights into functional myelin biology. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4643-8. [PubMed]
  17. Yang SH, Liu R, Perez EJ, Wen Y, Stevens SM Jr, Valencia T, Brun-Zinkernagel AM, Prokai L, Will Y, Dykens J, Koulen P, Simpkins JW. Mitochondrial localization of estrogen receptor {beta}  Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4130-4135.  [PubMed]
  18. Kumar JK, Tabor S, Richardson CC. Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli. Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3759-64. [PubMed]
  19. Nedelkov D, Tubbs KA, Niederkofler EE, Kiernan UA, Nelson RW. High-Throughput Comprehensive Analysis of Human Plasma Proteins: A Step toward Population Proteomics. Anal Chem. 2004 Mar 15;76(6):1733-7. [PubMed]
  20. Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjolander K, Gruissem W, Baginsky S. The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol. 2004 Mar 9;14(5):354-62. [PubMed]
  21. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93.  [PubMed]
  22. Prudhomme W, Daley GQ, Zandstra P, Lauffenburger DA. Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2900-5. [PubMed]
  23. Balmer Y, Vensel WH, Tanaka CK, Hurkman WJ, Gelhaye E, Rouhier N, Jacquot JP, Manieri W, Schurmann P, Droux M, Buchanan BB. Thioredoxin links redox to the regulation of fundamental processes of plant mitochondria.Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2642-7. [PubMed]
  24. Wagner V, Fiedler M, Markert C, Hippler M, Mittag M. Functional proteomics of circadian expressed proteins from Chlamydomonas reinhardtii. FEBS Lett. 2004 Feb 13;559(1-3):129-35. [PubMed]
  25. Brehmer D, Godl K, Zech B, Wissing J, Daub H. Proteome-wide identification of cellular targets affected by bisindolylmaleimide-type protein kinase C inhibitors. Mol Cell Proteomics. 2004 Feb 9 [Epub ahead of print] [PubMed]
  26. MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR. Gene expression in yeast responding to mating pheromone: Analysis by high-resolution translation state analysis and quantitative proteomics. Mol Cell Proteomics. 2004 Feb 6 [Epub ahead of print] [PubMed]
  27. Evans CA, Tonge R, Blinco D, Pierce A, Shaw J, Lu Y, Hamzah HG, Gray A, Downes CP, Gaskell SJ, Spooncer E, Whetton AD. Comparative proteomics of primitive hematopoietic cell populations reveals differences in expression of proteins regulating motility. Blood. 2004 Feb 5 [Epub ahead of print] [PubMed]
  28. Mostertz J, Scharf C, Hecker M, Homuth G. Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology. 2004 Feb;150(Pt 2):497-512. [PubMed]
  29. Thorne GD, Hilliard GM, Paul RJ. Vascular oxygen sensing: detection of novel candidates by proteomics and organ culture. J Appl Physiol. 2004 Feb; 96(2): 802-8. [PubMed]
  30. Jin K, Mao XO, Cottrell B, Schilling B, Xie L, Row RH, Sun Y, Peel A, Childs J, Gendeh G, Gibson BW, Greenberg DA. Proteomic and immunochemical characterization of a role for stathmin in adult neurogenesis. FASEB J. 2004 Feb;18(2):287-99. [PubMed]
  31. Campo S, Carrascal M, Coca M, Abian J, San Segundo B. The defense response of germinating maize embryos against fungal infection: A proteomics approach. Proteomics. 2004 Feb;4(2):383-96. [PubMed]
  32. Lonosky PM, Zhang X, Honavar VG, Dobbs DL, Fu A, Rodermel SR. A proteomic analysis of maize chloroplast biogenesis. Plant Physiol. 2004 Feb;134(2):560-74. [PubMed]
  33. Jiang XS, Zhou H, Zhang L, Sheng QH, Li SJ, Li L, Hao P, Li YX, Xia QC, Wu JR, Zeng R. A High-throughput approach for subcellular proteome: Identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mol Cell Proteomics. 2004 Jan 22 [Epub ahead of print] [PubMed]
  34. Sethuraman M, McComb ME, Heibeck T, Costello CE, Cohen RA. Isotope-coded affinity tag (ICAT) approach to identify and quantify oxidant-sensitive protein thiols. Mol Cell Proteomics. 2004 Jan 15 [Epub ahead of print] [PubMed]
  35. McLean L, Doherty MK, Deeming DC, Beynon RJ. A proteome analysis of the subcutaneous gel in avian hatchlings. Mol Cell Proteomics. 2004 Jan 13 [Epub ahead of print] [PubMed]
  36. Vierstraete E, Verleyen P, Baggerman G, D'Hertog W, Van Den Bergh G, Arckens L, De Loof A, Schoofs L. A proteomic approach for the analysis of instantly released wound and immune proteins in Drosophila melanogaster hemolymph. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2): 470-5. [PubMed]
  37. White SL, Gharbi S, Bertani MF, Chan HL, Waterfield MD, Timms JF. Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression. Br J Cancer. 2004 Jan 12;90(1):173-81. [PubMed]
  38. Purcell AW, Gorman JJ. Immunoproteomics: Mass spectrometry based methods to study the targets of the immune response. Mol Cell Proteomics. 2004 Jan 12 [Epub ahead of print] [PubMed]
  39. Anderson NL, Polanski M, Pieper R, Gatlin T, Tirumalai RS, Conrads TP, Veenstra TD, Adkins JN, Pounds JG, Fagan R, Lobley A. The human plasma proteome: A non-redundant list developed by combination of four separate sources. Mol Cell Proteomics. 2004 Jan 12 [Epub ahead of print] [PubMed]
  40. Korke R, Gatti Mde L, Lau AL, Lim JW, Seow TK, Chung MC, Hu WS. Large scale gene expression profiling of metabolic shift of mammalian cells in culture. J Biotechnol. 2004 Jan 8;107(1):1-17. [PubMed]
  41. Pinet F, Poirier F, Fuchs S, Tharaux PL, Caron M, Corvol P, Michel JB, Joubert-Caron R. Troponin T as a marker of differentiation revealed by proteomic analysis in renal arterioles. FASEB J. 2004 Jan 8 [Epub ahead of print] [PubMed]
  42. Gong L, Puri M, Unlu M, Young M, Robertson K, Viswanathan S, Krishnaswamy A, Dowd SR, Minden JS. Drosophila ventral furrow morphogenesis: a proteomic analysis. Development. 2004 Jan 7 [Epub ahead of print] [PubMed]
  43. Swatton JE, Prabakaran S, Karp NA, Lilley KS, Bahn S. Protein profiling of human postmortem brain using 2-dimensional fluorescence difference gel electrophoresis (2-D DIGE). Mol Psychiatry. 2004 Jan 6 [Epub ahead of print] [PubMed]
  44. Kim H, Page GP, Barnes S. Proteomics and mass spectrometry in nutrition research. Nutrition. 2004 Jan;20(1):155-165. [PubMed]
  45. Brand M, Ranish JA, Kummer NT, Hamilton J, Igarashi K, Francastel C, Chi TH, Crabtree GR, Aebersold R, Groudine M. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol. 2004 Jan; 11(1): 73-80.  [PubMed]
  46. Noel-Georis I, Vallaeys T, Chauvaux R, Monchy S, Falmagne P, Mergeay M, Wattiez R. Global analysis of the Ralstonia metallidurans proteome: Prelude for the large-scale study of heavy metal response. Proteomics. 2004 Jan; 4(1): 151-79. [PubMed]
  47. Corpillo D, Gardini G, Vaira AM, Basso M, Aime S, Accotto GP, Fasano M. Proteomics as a tool to improve investigation of substantial equivalence in genetically modified organisms: The case of a virus-resistant tomato. Proteomics. 2004 Jan; 4(1): 193-200. [PubMed]
  48. De Angelis M, Gobbetti M. Environmental stress responses in Lactobacillus: A review. Proteomics. 2004 Jan; 4(1): 106-22. [PubMed]
  49. Rautajoki K, Nyman TA, Lahesmaa R. Proteome characterization of human T helper 1 and 2 cells. Proteomics. 2004 Jan; 4(1): 84-92. [PubMed]
  50. McHardy AC, Puhler A, Kalinowski J, Meyer F. Comparing expression level-dependent features in codon usage with protein abundance: An analysis of 'predictive proteomics'. Proteomics. 2004 Jan; 4(1): 46-58. [PubMed]
  51. Poland J, Urbani A, Lage H, Schnolzer M, Sinha P. Study of the development of thermoresistance in human pancreatic carcinoma cell lines using proteome analysis. Electrophoresis. 2004 Jan;25(1):173-83. [PubMed]
  52. Sprenger RR, Speijer D, Back JW, De Koster CG, Pannekoek H, Horrevoets AJ. Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis. 2004 Jan;25(1):156-72. [PubMed]
  53. Herranen M, Battchikova N, Zhang P, Graf A, Sirpio S, Paakkarinen V, Aro EM. Towards Functional Proteomics of Membrane Protein Complexes in Synechocystis sp. PCC 6803. Plant Physiol. 2004 Jan;134(1):470-81. [PubMed]

Disease research

  1. Check E. Proteomics and cancer: running before we can walk? Nature. 2004 Jun 3;429(6991):496-7. [PubMed]
  2. Zang L, Toy DP, Hancock WS, Sgroi DC, Karger BL. Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 16O/18O isotopic labeling. J Proteome Res. 2004 May-Jun;3(3):604-12. [PubMed]
  3. te Pas MF, Claes F. Functional genomics and proteomics for infectious diseases in the post-genomics era. Lancet. 2004 Apr 24;363(9418):1337. [PubMed]
  4. Borozdenkova S, Westbrook JA, Patel V, Wait R, Bolad I, Burke MM, Bell AD, Banner NR, Dunn MJ, Rose ML. Use of proteomics to discover novel markers of cardiac allograft rejection. J Proteome Res. 2004 Mar-Apr;3(2):282-8. [PubMed]
  5. Johnson JR, Florens L, Carucci DJ, Yates JR 3rd. Proteomics in malaria. J Proteome Res. 2004 Mar-Apr;3(2):296-306.[PubMed]
  6. Perlson E, Medzihradszky KF, Darula Z, Munno DW, Syed NI, Burlingame AL, Fainzilber M. Differential proteomics reveals multiple components in retrogradely transported axoplasm after nerve injury. Mol Cell Proteomics. 2004 Feb 18 [Epub ahead of print] [PubMed]
  7. Pan Y, Kislinger T, Gramolini AO, Zvaritch E, Kranias EG, MacLennan DH, Emili A. Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics. Proc Natl Acad Sci U S A. 2004 Feb 13 [Epub ahead of print] [PubMed]
  8. Schwartz SA, Weil RJ, Johnson MD, Toms SA, Caprioli RM. Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression. Clin Cancer Res. 2004 Feb 1;10(3):981-7. [PubMed]
  9. Simpson DM, Beynon RJ, Robertson DH, Loughran MJ, Haywood S. Copper-associated liver disease: A proteomics study of copper challenge in a sheep model. Proteomics. 2004 Feb;4(2):524-36. [PubMed]
  10. Celis JE, Gromov P, Cabezon T, Moreira JM, Ambartsumian N, Sandelin K, Rank F, Gromova I. Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment: A novel resource forbiomarker and therapeutic target discovery. Mol Cell Proteomics. 2004 Jan 30 [Epub ahead of print] [PubMed]
  11. Bowler RP, Duda B, Chan ED, Enghild JJ, Ware LB, Matthay MA, Duncan MW. A PROTEOMIC ANALYSIS OF PULMONARY EDEMA FLUID AND PLASMA IN PATIENTS WITH ACUTE LUNG INJURY. Am J Physiol Lung Cell Mol Physiol. 2004 Jan 23 [Epub ahead of print] [PubMed]
  12. Dotzlaw H, Schulz M, Eggert M, Neeck G. A pattern of protein expression in peripheral blood mononuclear cells distinguishes rheumatoid arthritis patients from healthy individuals. Biochim Biophys Acta. 2004 Jan 14;1696(1):121-9. [PubMed]
  13. Mocellin S, Riccardo Rossi C, Traldi P, Nitti D, Lise M. Molecular oncology in the post-genomic era: the challenge of proteomics. Trends Mol Med. 2004 Jan; 10(1): 24-32. [PubMed]
  14. He QY, Chen J, Kung HF, Yuen AP, Chiu JF. Identification of tumor-associated proteins in oral tongue squamous cell carcinoma by proteomics. Proteomics. 2004 Jan; 4(1): 271-8. [PubMed]
  15. Xiao X, Liu D, Tang Y, Guo F, Xia L, Liu J, He D.  Development of proteomic patterns for detecting lung cancer. Dis Markers. 2003-2004;19(1):33-9. [PubMed]
  16. Dobos KM, Spencer JS, Orme IM, Belisle JT. Proteomic approaches to antigen discovery. Methods Mol Med. 2004;94:3-17. [PubMed]

Clinical application

  1. Oh P, Li Y, Yu J, Durr E, Krasinska KM, Carver LA, Testa JE, Schnitzer JE. Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature. 2004 Jun 10;429(6992):629-35. [PubMed]
  2. Proteomic diagnostics tested. Nature. 2004 Jun 3;429(6991):487.[PubMed]
  3. Gerton GL, Fan XJ, Chittams J, Sammel M, Hummel A, Strauss JF, Barnhart K. A serum proteomics approach to the diagnosis of ectopic pregnancy. Ann N Y Acad Sci. 2004 Jun;1022:306-16. [PubMed]
  4. Johann DJ Jr, McGuigan MD, Patel AR, Tomov S, Ross S, Conrads TP, Veenstra TD, Fishman DA, Whiteley GR, Petricoin EF 3rd, Liotta LA. Clinical Proteomics and Biomarker Discovery. Ann N Y Acad Sci. 2004 Jun;1022:295-305. [PubMed]
  5. Rai AJ, Chan DW. Cancer Proteomics: Serum Diagnostics for Tumor Marker Discovery. Ann N Y Acad Sci. 2004 Jun;1022:286-294. [PubMed]
  6. Taback B, Hoon DS. Circulating Nucleic Acids and Proteomics of Plasma/Serum: Clinical Utility. Ann N Y Acad Sci. 2004 Jun;1022:1-8. [PubMed]
  7. Kaiser T, Kamal H, Rank A, Kolb HJ, Holler E, Ganser A, Hertenstein B, Mischak H, Weissinger EM. Proteomics applied to the clinical follow up of patients after allogeneic hematopoietic stem cell transplantation. Blood. 2004 Mar 30 [Epub ahead of print] [PubMed]
  8. Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst. 2004 Mar 3;96(5):353-6. [PubMed]
  9. Wilson JF. The promise of disease proteomics: faster detection, diagnosis, and drug development. Ann Intern Med. 2004 Feb 17;140(4):317-9. [PubMed]
  10. Rosenblatt KP, Bryant-Greenwood P, Killian JK, Mehta A, Geho D, Espina V, Petricoin EF, Liotta LA. Serum Proteomics in Cancer Diagnosis and Management. Annu Rev Med. 2004 Feb;55:97-112. [PubMed]
  11. Zolg JW, Langen H. How industry is approaching the search for new diagnostic markers and biomarkers. Mol Cell Proteomics. 2004 Jan 28 [Epub ahead of print] [PubMed]
  12. Hanash S. HUPO initiatives relevant to clinical proteomics. Mol Cell Proteomics. 2004 Jan 27 [Epub ahead of print] [PubMed]
  13. Cristea IM, Gaskell SJ, Whetton AD. Proteomics techniques and their application to hematology. Blood. 2004 Jan 15 [Epub ahead of print] [PubMed]
  14. Dotzlaw H, Schulz M, Eggert M, Neeck G. A pattern of protein expression in peripheral blood mononuclear cells distinguishes rheumatoid arthritis patients from healthy individuals. Biochim Biophys Acta. 2004 Jan 14;1696(1):121-9. [PubMed]

Pharmacogenomics

  1. Walgren JL, Thompson DC. Application of proteomic technologies in the drug development process. Toxicol Lett. 2004 Apr 1;149(1-3):377-85. [PubMed]
  2. Jain KK. Role of pharmacoproteomics in the development of personalized medicine. Pharmacogenomics. 2004 Apr;5(3):331-6. [PubMed]
  3. Weston AD, Hood L. Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res. 2004 Mar-Apr;3(2):179-96. [PubMed]
  4. Petricoin E, Wulfkuhle J, Espina V, Liotta LA. Clinical proteomics: revolutionizing disease detection and patient tailoring therapy. J Proteome Res. 2004 Mar-Apr;3(2):209-17. [PubMed]
  5. Wilson JF. The promise of disease proteomics: faster detection, diagnosis, and drug development. Ann Intern Med. 2004 Feb 17;140(4):317-9. [PubMed]
  6. Khawaja X, Xu J, Liang JJ, Barrett JE. Proteomic analysis of protein changes developing in rat hippocampus after chronic antidepressant treatment: Implications for depressive disorders and future therapies. J Neurosci Res. 2004 Feb 15; 75(4): 451-60. [PubMed]
  7. Lowe D, Jermutus L. Combinatorial protein biochemistry for therapeutics and proteomics. Curr Pharm Biotechnol. 2004 Feb;5(1):17-27. [PubMed]
  8. Gerner C. Screening for Disease-Markers and Investigating Drug Effects by Proteome Profiling: Can it Meet Expectations? Comb Chem High Throughput Screen. 2004 Feb;7(1):1-9. [PubMed]
  9. Bodovitz S, Joos T. The proteomics bottleneck: strategies for preliminary validation of potential biomarkers and drug targets. Trends Biotechnol. 2004 Jan;22(1):4-7. [PubMed]

Protein-protein interaction

  1. Schulze WX, Mann M. A novel proteomic screen for peptide-protein interactions. J Biol Chem. 2004 Mar 12; [PubMed]
  2. Przulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics. 2004 Feb 12;20(3):340-8. [PubMed]
  3. Malek JA, Wierzbowski JM, Tao W, Bosak SA, Saranga DJ, Doucette-Stamm L, Smith DR, McEwan PJ, McKernan KJ. Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica. Nucleic Acids Res. 2004 Feb 10;32(3):1059-1064. [PubMed]
  4. Cho S, Park SG, Lee do H, Park BC. Protein-protein interaction networks: from interactions to networks. J Biochem Mol Biol. 2004 Jan 31;37(1):45-52. [PubMed]
  5. Uetz P, Pankratz MJ. Protein interaction maps on the fly. Nat Biotechnol. 2004 Jan;22(1):43-4. [PubMed]

Network/pathway reconstruction and analysis

  1. Sontag E, Kiyatkin A, Kholodenko BN. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics. 2004 Mar 22 [Epub ahead of print] [PubMed]
  2. Fernandez A, Scott R, Berry RS. The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2823-7. [PubMed]
  3. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93.  [PubMed]
  4. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M. A Map of the Interactome Network of the Metazoan C. elegans. Science. 2004 Jan 23; 303(5657): 540-3.[PubMed][Supporting Online Material] 

Structural genomics

  1. Arakaki AK, Zhang Y, Skolnick J. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics. 2004 May 1;20(7):1087-96. [PubMed]
  2. Pechkova E, Nicolini C. Protein nanocrystallography: a new approach to structural proteomics. Trends Biotechnol. 2004 Mar;22(3):117-22. [PubMed]
  3. Walian P, Cross TA, Jap BK. Structural genomics of membrane proteins. Genome Biol. 2004;5(4):215. [PubMed]
  4. Yakunin AF. et al., Structural proteomics: a tool for genome annotation. Curr Opin Chem Biol.  2004 Feb [PubMed]
  5. Gerstein M et al., Exploring the range of protein flexibility, from a structural proteomics perspective. Curr Opin Chem Biol.  2004 Feb [PubMed]
  6. Jung JW, Lee W. Structure-based functional discovery of proteins: structural proteomics. J Biochem Mol Biol. 2004 Jan 31;37(1):28-34. [PubMed]
  7. Ippel JH, Pouvreau L, Kroef T, Gruppen H, Versteeg G, Van Den Putten P, Struik PC, Van Mierlo CP. In vivo uniform 15N-isotope labelling of plants: Using the greenhouse for structural proteomics. Proteomics. 2004 Jan; 4(1): 226-34. [PubMed]
  8. Deutzmann R. Structural characterization of proteins and peptides. Methods Mol Med. 2004;94:269-97. [PubMed]
  9. Segelke BW, Schafer J, Coleman MA, Lekin TP, Toppani D, Skowronek KJ, Kantardjieff KA, Rupp B. Laboratory scale structural genomics. J Struct Funct Genomics. 2004;5(1-2):147-57. [PubMed]

Technical developments

  1. Ramstrom M, Bergquist J. Miniaturized proteomics and peptidomics using capillary liquid separation and high resolution mass spectrometry. FEBS Lett. 2004 Jun 1;567(1):92-5. [PubMed]
  2. Parker KC, Patterson D, Williamson B, Marchese J, Graber A, He F, Jacobson A, Juhasz P, Martin SA. Depth of proteome issues: A yeast ICAT reagent study. Mol Cell Proteomics. 2004 Mar 28 [Epub ahead of print] [PubMed]
  3. Ovaa H, Kessler BM, Rolen U, Galardy PJ, Ploegh HL, Masucci MG. Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2253-8. [PubMed]
  4. Lue RY, Chen GY, Hu Y, Zhu Q, Yao SQ. Versatile protein biotinylation strategies for potential high-throughput proteomics. J Am Chem Soc. 2004 Feb 4;126(4):1055-62. [PubMed]
  5. Del Val C, Mehrle A, Falkenhahn M, Seiler M, Glatting KH, Poustka A, Suhai S, Wiemann S. High-throughput protein analysis integrating bioinformatics and experimental assays. Nucleic Acids Res. 2004 Feb 03;32(2):742-8. [PubMed]
  6. Mitsopoulos G. et al., Tagged library approach to chemical genomics and proteomics. Curr Opin Chem Biol.  2004 Feb [PubMed]
  7. Pelech S, Tracking Cell Signaling Protein Expression and Phosphorylation by Innovative Proteomic Solutions. Curr Pharm Biotechnol. 2004 Feb;5(1):45-67. [PubMed]
  8. Jessani N.et al., The development and application of methods for activity-based protein profiling. Curr Opin Chem Biol.  2004 Feb [PubMed]
  9. Zhang H et al., Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr Opin Chem Biol.  2004 Feb [PubMed]
  10. Dumas-Gaudot E, Amiour N, Weidmann S, Bestel-Corre G, Valot B, Lenogue S, Gianinazzi-Pearson V, Gianinazzi S. A technical trick for studying proteomics in parallel to transcriptomics in symbiotic root-fungus interactions. Proteomics. 2004 Feb;4(2):451-3. [PubMed]
  11. Blonder J, Conrads TP, Yu LR, Terunuma A, Janini GM, Issaq HJ, Vogel JC, Veenstra TD. A detergent- and cyanogen bromide-free method for integral membrane proteomics: Application to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics. 2004 Jan;4(1):31-45. [PubMed]
  12. Bradbury AR, Velappan N, Verzillo V, Ovecka M, Marzari R, Sblattero D, Chasteen L, Siegel R, Pavlik P. Antibodies in proteomics. Methods Mol Biol. 2004;248:519-46. [PubMed]
  13. Purvine S, Picone AF, Kolker E. Standard mixtures for proteome studies. OMICS. 2004 Spring;8(1):79-92. [PubMed]
  14. Li J, Tremblay TL, Harrison J, Thibault P. Integrated system for rapid proteomics analyses using microfluidic devices coupled to nanoelectrospray mass spectrometry. Methods Mol Biol. 2004;276:305-24. [PubMed]

Protein expression techniques

  1. Jackson AM, Boutell J, Cooley N, He M. Cell-free protein synthesis for proteomics. Brief Funct Genomic Proteomic. 2004 Feb;2(4):308-19. [PubMed]
  2. Sitaraman K, Esposito D, Klarmann G, Le Grice SF, Hartley JL, Chatterjee DK. A novel cell-free protein synthesis system. J Biotechnol. 2004 Jun 10;110(3):257-63. [PubMed]
  3. Hust M, Dubel S. Mating antibody phage display with proteomics. Trends Biotechnol. 2004 Jan;22(1):8-14.  [PubMed]
  4. Ogorelkova M, Elahi SM, Gagnon D, Massie B. DNA delivery to cells in culture: generation of adenoviral libraries for high-throughput functional screening. Methods Mol Biol. 2004;246:15-27. [PubMed]
  5. Kigawa T, Yabuki T, Matsuda N, Matsuda T, Nakajima R, Tanaka A, Yokoyama S. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J Struct Funct Genomics. 2004;5(1-2):63-8. [PubMed]

2D gel; Protein purification and chromatographic techniques

  1. Nagele E, Vollmer M, Horth P. Improved 2D Nano-LC/MS for Proteomics Applications: A Comparative Analysis Using Yeast Proteome. J Biomol Tech. 2004 Jun;15(2):134-43. [PubMed]
  2. Church S. Advances in two-dimensional gel matching technology. Biochem Soc Trans. 2004 Jun;32(Pt 3):511-6. [PubMed]
  3. Wienkoop S, Glinski M, Tanaka N, Tolstikov V, Fiehn O, Weckwerth W. Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins. Rapid Commun Mass Spectrom. 2004;18(6):617-28. [PubMed]
  4. Lee H, Yi EC, Wen B, Reily TP, Pohl L, Nelson S, Aebersold R, Goodlett DR. Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Apr 15;803(1):101-10. [PubMed]
  5. Nomura E, Katsuta K, Ueda T, Toriyama M, Mori T, Inagaki N. Acid-labile surfactant improves in-sodium dodecyl sulfate polyacrylamide gel protein digestion for matrix-assisted laser desorption/ionization mass spectrometric peptide mapping. J Mass Spectrom. 2004 Feb;39(2):202-7. [PubMed]
  6. Larsen MR, Graham ME, Robinson PJ, Roepstorff P. Improved detection of hydrophilic phosphopeptides using graphite powder micro-columns and mass spectrometry: Evidence for in vivo doubly phosphorylated dynamin I and dynamin III. Mol Cell Proteomics. 2004 Feb 2 [Epub ahead of print] [PubMed]
  7. Masuda M, Toriumi C, Santa T, Imai K. Fluorogenic Derivatization Reagents Suitable for Isolation and Identification of Cysteine-Containing Proteins Utilizing High-Performance Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem. 2004 Feb 1;76(3):728-735. [PubMed]
  8. Guttman A, Varoglu M, Khandurina J.  Multidimensional separations in the pharmaceutical arena. Drug Discov Today. 2004 Feb 1;9(3):136-44.[PubMed]
  9. Fountoulakis M, Juranville JF, Tsangaris G, Suter L. Fractionation of liver proteins by preparative electrophoresis. Amino Acids. 2004 Feb;26(1):27-36. [PubMed]
  10. Van den Bergh G et al., Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics. Curr Opin Biotechnol. 2004 Feb; [PubMed]
  11. Van den Bergh G, Arckens L. Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics. Curr Opin Biotechnol. 2004 Feb;15(1):38-43. [PubMed]
  12. Belov ME, Anderson GA, Wingerd MA, Udseth HR, Tang K, Prior DC, Swanson KR, Buschbach MA, Strittmatter EF, Moore RJ, Smith RD. An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics. J Am Soc Mass Spectrom. 2004 Feb;15(2):212-32. [PubMed]
  13. Corton M, Villuendas G, Botella JI, San Millan JL, Escobar-Morreale HF, Peral B. Improved resolution of the human adipose tissue proteome at alkaline and wide range pH by the addition of hydroxyethyl disulfide. Proteomics. 2004 Feb;4(2):438-41. [PubMed]
  14. iang L, He L, Fountoulakis M. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J Chromatogr A. 2004 Jan 16;1023(2):317-20. [PubMed]
  15. Jacquot JP, Rouhier N, Navrot N, Decottignies JP. Generation of polyclonal antibodies against multiple proteins in a single rabbit and subsequent isolation of the specific immunoglobulins as a tool for proteomics research. Biotechnol Appl Biochem. 2004 Jan 15 [Epub ahead of print] [PubMed]
  16. Lee WC, Lee KH. Applications of affinity chromatography in proteomics. Anal Biochem. 2004 Jan 1;324(1):1-10. [PubMed]
  17. Shen Y, Tolic N, Masselon C, Pasa-Tolic L, Camp DG 2nd, Hixson KK, Zhao R, Anderson GA, Smith RD. Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS. Anal Chem. 2004 Jan 1;76(1):144-154. [PubMed]
  18. Bernard KR, Jonscher KR, Resing KA, Ahn NG. Methods in Functional Proteomics: Two-Dimensional Polyacrylamide Gel Electrophoresis With Immobilized pH Gradients In-Gel Digestion and Identification of Proteins by Mass Spectrometry. Methods Mol Biol. 2004;250:263-82. [PubMed]
  19. Zuo X, Speicher DW. Microscale solution isoelectrofocusing: a sample prefractionation method for comprehensive proteome analysis. Methods Mol Biol. 2004;244:361-76. [PubMed]
  20. Dunn MJ. Electroblotting of proteins from polyacrylamide gels. Methods Mol Biol. 2004;244:345-52. [PubMed]

Mass spectrometry

  1. Nagele E, Vollmer M, Horth P. Improved 2D Nano-LC/MS for Proteomics Applications: A Comparative Analysis Using Yeast Proteome. J Biomol Tech. 2004 Jun;15(2):134-43. [PubMed]
  2. Yates JR. Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct. 2004 Jun;33:297-316. [PubMed]
  3. Venable JD, Yates JR 3rd. Impact of ion trap tandem mass spectra variability on the identification of peptides. Anal Chem. 2004 May 15;76(10):2928-37. [PubMed]
  4. Zaia J. Mass spectrometry of oligosaccharides. Mass Spectrom Rev. 2004 May;23(3):161-227. [PubMed]
  5. Bogdanov B, Smith RD. Proteomics by FTICR mass spectrometry: Top down and bottom up. Mass Spectrom Rev. 2004 Mar 30 [Epub ahead of print] [PubMed]
  6. Belov ME, Anderson GA, Wingerd MA, Udseth HR, Tang K, Prior DC, Swanson KR, Buschbach MA, Strittmatter EF, Moore RJ, Smith RD. An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics. J Am Soc Mass Spectrom. 2004 Feb;15(2):212-32. [PubMed]
  7. Wenner BR, Lynn BC. Factors that affect ion trap data-dependent MS/MS in proteomics. J Am Soc Mass Spectrom. 2004 Feb;15(2):150-7. [PubMed]
  8. Shen Y, Tolic N, Masselon C, Pasa-Tolic L, Camp DG 2nd, Hixson KK, Zhao R, Anderson GA, Smith RD. Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS. Anal Chem. 2004 Jan 1;76(1):144-154. [PubMed]
  9. Cargile BJ, Bundy JL, Grunden AM, Stephenson JL Jr. Synthesis/Degradation Ratio Mass Spectrometry for Measuring Relative Dynamic Protein Turnover. Anal Chem. 2004 Jan 1;76(1):86-97. [PubMed]

Protein-protein interaction study

  1. Osman A. Yeast two-hybrid assay for studying protein-protein interactions. Methods Mol Biol. 2004;270:403-22. [PubMed]

Protein function study

  1. Daub H, Godl K, Brehmer D, Klebl B, Muller G. Evaluation of kinase inhibitor selectivity by chemical proteomics. Assay Drug Dev Technol. 2004 Apr;2(2):215-24. [PubMed]

Post-translational modification study

  1. Shi X, Belton RJ Jr, Burkin HR, Vieira AP, Miller DJ. A proteomic approach to identify phosphoproteins encoded by cDNA libraries. Anal Biochem. 2004 Jun 15;329(2):289-92. [PubMed]
  2. Appel RD, Bairoch A. Post-translational modifications: A challenge for proteomics and bioinformatics. Proteomics. 2004 Jun;4(6):1525-1526. [PubMed]
  3. Jensen ON. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol.  2004 Feb [PubMed]
  4. Seo J, Lee KJ. Post-translational modifications and their biological functions: proteomic analysis and systematic approaches. J Biochem Mol Biol. 2004 Jan 31;37(1):35-44. [PubMed]

Data analysis

  1. Hoglund A, Kohlbacher O. From sequence to structure and back again: approaches for predicting protein-DNA binding. Proteome Sci. 2004 Jun 17;2(1):3. [PubMed]
  2. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004 Jun 12;20(9):1466-7. [PubMed]
  3. Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics. 2004 Jun;4(6):1633-49. [PubMed]
  4. 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 Mar 25 [Epub ahead of print] [PubMed]
  5. Chou KC, Cai YD. Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition. J Cell Biochem. 2004 Apr 15;91(6):1197-203. [PubMed]
  6. Beer I, Barnea E, Ziv T, Admon A. Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics. 2004 Apr;4(4):950-60. [PubMed]
  7. Weiller GF, Caraux G, Sylvester N. The modal distribution of protein isoelectric points reflects amino acid properties rather than sequence evolution. Proteomics. 2004 Apr;4(4):943-9. [PubMed]
  8. Yang ZR, Chou KC. Bio-support vector machines for computational proteomics. Bioinformatics. 2004 Mar 22;20(5):735-41. [PubMed]
  9. Ma HW, Zhao XM, Yuan YJ, Zeng AP. Decomposition of metabolic network based on the global connectivity structure of reaction graph. Bioinformatics. 2004 Mar 22 [Epub ahead of print] [PubMed]
  10. Gilchrist MA, Salter LA, Wagner A. A statistical framework for combining and interpreting proteomic datasets. Bioinformatics. 2004 Mar 22;20(5):689-700. [PubMed]
  11. Baczek T, Bucinski A, Ivanov AR, Kaliszan R. Artificial Neural Network Analysis for Evaluation of Peptide MS/MS Spectra in Proteomics. Anal Chem. 2004 Mar 15;76(6):1726-1732. [PubMed]
  12. Nesvizhskii AI, Aebersold R. Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today. 2004 Feb 15;9(4):173-81.[PubMed]
  13. Cai YD, Chou KC. Predicting subcellular localization of proteins in a hybridization space. Bioinformatics. 2004 Feb 5 [Epub ahead of print] [PubMed]
  14. Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat Biotechnol. 2004 Feb;22(2):214-9. [PubMed]
  15. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb;22(2):177-83. [PubMed]
  16. Blueggel M, Chamrad D, Meyer HE. Bioinformatics in proteomics. Curr Pharm Biotechnol. 2004 Feb;5(1):79-88. [PubMed]
  17. Orchard S, Hermjakob H, Julian RK Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R. Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics. 2004 Feb;4(2):490-1. [PubMed]
  18. Yang ZR, Chou KC. Bio-support vector machines for computational proteomics. Bioinformatics. 2004 Jan 29 [Epub ahead of print] [PubMed]
  19. Ravichandran V, Lubell J, Vasquez GB, Lemkin P, Sriram RD, Gilliland GL. Ongoing development of two-dimensional polyacrylamide gel electrophoresis data standards. Electrophoresis. 2004 Jan;25(2):297-308. [PubMed]
  20. Kempka M, Sjodahl J, Bjork A, Roeraade J. Improved method for peak picking in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(11):1208-12. [PubMed]

Software

  1. Young N, Chang Z, Wishart DS. GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. Bioinformatics. 2004 Apr 12;20(6):976-8.  [PubMed]
  2. Demine R, Walden P. Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(8):907-13. [PubMed]
  3. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004 Feb 19 [Epub ahead of print] [PubMed]
  4. Wang J, Caron C, Mistou MY, Gitton C, Trubuil A. PARIS: a proteomic analysis and resources indexation system. Bioinformatics. 2004 Jan 1;20(1):133-5. [PubMed]

Database

  1. Garavelli JS. The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics. 2004 Jun;4(6):1527-33. [PubMed]
  2. Pleissner KP, Eifert T, Buettner S, Schmidt F, Boehme M, Meyer TF, Kaufmann SH, Jungblut PR. Web-accessible proteome databases for microbial research. Proteomics. 2004 May;4(5):1305-13. [PubMed]
  3. Traxler E, Bayer E, Stockl J, Mohr T, Lenz C, Gerner C. Towards a standardized human proteome database: Quantitative proteome profiling of living cells. Proteomics. 2004 May;4(5):1314-23. [PubMed]
  4. Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM. The need for a public proteomics repository. Nat Biotechnol. 2004 Apr;22(4):471-2. [PubMed]
  5. Orchard S, Hermjakob H, Julian RK Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R. Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics. 2004 Feb;4(2):490-1. [PubMed]
  6. Kortemme T. et al., Computational design of protein–protein interactions. Curr Opin Chem Biol.  2004 Feb [PubMed]
  7. Nesvizhskii AI, Aebersold R. Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today. 2004 Feb 15;9(4):173-81.[PubMed]
  8. Nucleic Acid Research January 1, 2004 issue - The Molecular Biology Database Collection - The link to the complete issue

last updated: 7 Aug 2004
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