My proteomics journal watch - year 2003 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. Lee PS, Lee KH. Escherichia coli-a model system that benefits from and contributes to the evolution of proteomics. Biotechnol Bioeng. 2003 Dec 30;84(7):801-14. [PubMed]
2. Hegde PS, White IR, Debouck C. Interplay of transcriptomics and proteomics. Curr Opin Biotechnol. 2003 Dec;14(6):647-51. [PubMed]
3. Service RF. Proteomics. A sharper focus. Science. 2003 Nov 21;302(5649):1318. [PubMed]
4. Service RF. Proteomics. Public projects gear up to chart the protein landscape. Science. 2003 Nov 21;302(5649):1316-8. [PubMed]
5. Joos T, Bodovitz S. Multidimensional proteomics. Drug Discov Today. 2003 Oct 1;8(19):879-80. [PubMed]
6. Thornton J. The proteome and the metabolome. Bioinformatics. 2003 Oct;19 Suppl 2:II237. [PubMed]
7. Patterson SD. Proteomics: evolution of the technology. Biotechniques. 2003 Sep;35(3):440-4. [PubMed]
8. Genomics & proteomics. Nat Biotechnol. 2003 Sep;21(9):1107. [PubMed]
9. Li WW, Quinn GB, Alexandrov NN, Bourne PE, Shindyalov IN. A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biol. 2003 Aug;4(8):R51. [PubMed]
10. Gershon D. Proteomics technologies: probing the proteome. Nature. 2003 Jul 31;424(6948):581-7. [PubMed]
11. Jain K. Proteomics and Protein Arrays Europa. Pharmacogenomics. 2003 Jul;4(4):383-385. [PubMed]
12. Orchard S, Hermjakob H, Apweiler R. The proteomics standards initiative. Proteomics. 2003 Jul;3(7):1374-6. [PubMed]
    

Application

1. Simpson JC, Pepperkok R. Localizing the proteome. Genome Biol. 2003;4(12):240.  [PubMed]
2. Brunet S, Thibault P, Gagnon E, Kearney P, Bergeron JJ, Desjardins M. Organelle proteomics: looking at less to see more. Trends Cell Biol. 2003 Dec;13(12):629-38. [PubMed]
3. Rakwal R, Agrawal GK. Rice proteomics: Current status and future perspectives. Electrophoresis. 2003 Oct;24(19-20):3378-89. [PubMed]
4. Dobos KM, Spencer JS, Orme IM, Belisle JT. Proteomic Approaches to Antigen Discovery. Methods Mol Med. 2003;:3-18. [PubMed]

Basic Science Studies

1. Paron I, D'Elia A, D'Ambrosio C, Scaloni A, D'Aurizio F, Prescott A, Damante G, Tell G. A proteomic approach to identify early molecular targets of oxidative stress in human epithelial lens cells. Biochem J. 2003 Dec 16 [Epub ahead of print] [PubMed]
2. Keightley JA, Shang L, Kinter M. Proteomic analysis of oxidative stress-resistant cells: A specific role for aldose reductase overexpression in cytoprotection. Mol Cell Proteomics. 2003 Dec 15 [Epub ahead of print] [PubMed]
3. Godl K, Wissing J, Kurtenbach A, Habenberger P, Blencke S, Gutbrod H, Salassidis K, Stein-Gerlach M, Missio A, Cotten M, Daub H. An efficient proteomics method to identify the cellular targets of protein kinase inhibitors. Proc Natl Acad Sci U S A. 2003 Dec 10 [Epub ahead of print] [PubMed][pdf]
4. Laragione T, Bonetto V, Casoni F, Massignan T, Bianchi G, Gianazza E, Ghezzi P. Redox regulation of surface protein thiols: Identification of integrin {alpha}-4 as a molecular target by using redox proteomics. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14737-14741. [PubMed] [PDF]
5. Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, Mann M. Proteomic characterization of the human centrosome by protein correlation profiling. Nature. 2003 Dec 4;426(6966):570-4. [PubMed]
6. Grinyer J, McKay M, Herbert B, Nevalainen H. Fungal proteomics: mapping the mitochondrial proteins of a Trichoderma harzianum strain applied for biological control. Curr Genet. 2003 Dec 2 [Epub ahead of print] [PubMed]
7. Arevalo-Ferro C, Hentzer M, Reil G, Gorg A, Kjelleberg S, Givskov M, Riedel K, Eberl L. Identification of quorum-sensing regulated proteins in the opportunistic pathogen Pseudomonas aeruginosa by proteomics. Environ Microbiol. 2003 Dec;5(12):1350-1369. [PubMed]
8. Hazbun TR, Malmstrom L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, Yates JR 3rd, Davis TN. Assigning function to yeast proteins by integration of technologies. Mol Cell. 2003 Dec;12(6):1353-65. [PubMed]
9. Unwin RD, Gaskell SJ, Evans CA, Whetton AD. The potential for proteomic definition of stem cell populations. Exp Hematol. 2003 Dec;31(12):1147-59. [PubMed]
10. Whelan SA, Hart GW. Proteomic approaches to analyze the dynamic relationships between nucleocytoplasmic protein glycosylation and phosphorylation. Circ Res. 2003 Nov 28;93(11):1047-58. [PubMed]
11. Levy F, Bulet P, Ehret-Sabatier L. Proteomic analysis of the systemic immune response of Drosophila. Mol Cell Proteomics. 2003 Nov 28 [Epub ahead of print] [PubMed]
12. Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, Bolouri MS, Ray HN, Sihag S, Kamal M, Patterson N, Lander ES, Mann M. Integrated Analysis of Protein Composition, Tissue Diversity, and Gene Regulation in Mouse Mitochondria. Cell. 2003 Nov 26;115(5):629-40.   [PubMed]
13. Baxter SM, Rosenblum JS, Knutson S, Nelson MR, Montimurro JS, Di Gennaro JA, Speir JA, Burbaum JJ, Fetrow JS. Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast. Mol Cell Proteomics. 2003 Nov 25 [Epub ahead of print] [PubMed]
14. McRedmond JP, Park SD, Reilly DF, Coppinger JA, Maguire PB, Shields DC, Fitzgerald DJ. Integration of proteomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes. Mol Cell Proteomics. 2003 Nov 25 [Epub ahead of print] [PubMed]
15. Ohlmeier S, Kastaniotis AJ, Hiltunen JK, Bergmann U. The yeast mitochondrial proteome - a study of fermentative and respiratory growth. J Biol Chem. 2003 Nov 3 [Epub ahead of print] [PubMed]
16. Vanrobaeys F, Devreese B, Lecocq E, Rychlewski L, De Smet L, Van Beeumen J. Proteomics of the dissimilatory iron-reducing bacterium Shewanella oneidensis MR-1, using a matrix-assisted laser desorption/ionization-tandem-time of flight mass spectrometer. Proteomics. 2003 Nov;3(11):2249-57. [PubMed]
17. Marko-Varga G, Berglund M, Malmstrom J, Lindberg H, Fehniger TE. Targeting hepatocytes from liver tissue by laser capture microdissection and proteomics expression profiling. Electrophoresis. 2003 Nov;24(21):3800-5. [PubMed]
18. Thompson LJ, Wang F, Proia AD, Peters KG, Jarrold B, Greis KD. Proteome analysis of the rat cornea during angiogenesis. Proteomics. 2003 Nov;3(11):2258-66. [PubMed]
19. Lefievre L, Barratt CL, Harper CV, Conner SJ, Flesch FM, Deeks E, Moseley FL, Pixton KL, Brewis IA, Publicover SJ. Physiological and proteomic approaches to studying prefertilization events in the human. Reprod Biomed Online. 2003 Oct-Nov;7(4):419-27. [PubMed]
20. Caldecott KW. Cell signaling. The BRCT domain: signaling with friends? Science. 2003 Oct 24;302(5645):579-80. [PubMed]
21. Manke IA, Lowery DM, Nguyen A, Yaffe MB. BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science. 2003 Oct 24;302(5645):636-9. [PubMed]
22. Wohlschlegel JA, Yates JR. Proteomics: where's Waldo in yeast? Nature. 2003 Oct 16;425(6959):671-2. [PubMed]
23. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature. 2003 Oct 16;425(6959):686-91. [PubMed]
24. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature. 2003 Oct 16;425(6959):737-41. [PubMed]
25. Weiler T, Sauder P, Cheng K, Ens W, Standing K, Wilkins JA. A proteomics-based approach for monoclonal antibody characterization. Anal Biochem. 2003 Oct 15;321(2):217-25. [PubMed]
26. Kikuchi M, Hatano N, Yokota S, Shimozawa N, Imanaka T, Taniguchi H. Proteomic analysis of rat liver peroxisome: Presence of peroxisome-specific isozyme of lon protease. J Biol Chem. 2003 Oct 15 [Epub ahead of print] [PubMed]
27. Woo HA, Kang SW, Kim HK, Yang KS, Chae HZ, Rhee SG. Reversible oxidation of the active site cysteine of peroxiredoxins to cysteine sulfinic acid: Immunoblot detection with antibodies specific for the hyperoxidized cysteine-containing sequence. J Biol Chem. 2003 Oct 14 [Epub ahead of print] [PubMed]
28. Schmidt F, Donahoe S, Hagens K, Mattow J, Schaible UE, Kaufmann SH, Aebersold R, Jungblut PR. Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope coded affinity tag technology. Mol Cell Proteomics. 2003 Oct 13 [Epub ahead of print] [PubMed]
29. Ritter B, Philie J, Girard M, Tung EC, Blondeau F, McPherson PS. Identification of a family of endocytic proteins that define a new alpha-adaptin ear-binding motif. EMBO Rep. 2003 Oct 10 [Epub ahead of print] [PubMed]
30. Li Kw K, Hornshaw MP, Van Der Schors RC, Watson R, Tate S, Casetta B, Jimenez CR, Gouwenberg Y, Gundelfinger ED, Smalla KH, Smit AB. Proteomics analysis of rat brain postsynaptic density: Implications of the diverse protein functional groups for the integration of synaptic physiology. J Biol Chem. 2003 Oct 7 [Epub ahead of print] [PubMed]
31. Ping P. Identification of novel signaling complexes by functional proteomics. Circ Res. 2003 Oct 3;93(7):595-603. [PubMed]
32. Keezer SM, Ivie SE, Krutzsch HC, Tandle A, Libutti SK, Roberts DD. Angiogenesis Inhibitors Target the Endothelial Cell Cytoskeleton through Altered Regulation of Heat Shock Protein 27 and Cofilin. Cancer Res. 2003 Oct 1;63(19):6405-12. [PubMed]
33. Akashi H. Metabolic economics and microbial proteome evolution. Bioinformatics. 2003 Oct;19 Suppl 2:II15. [PubMed]
34. Sonawane A, Kloppner U, Hovel S, Volker U, Rohm KH. Identification of Pseudomonas proteins coordinately induced by acidic amino acids and their amides: a two-dimensional electrophoresis study. Microbiology. 2003 Oct;149(Pt 10):2909-2918. [PubMed]
35. Hu W, Wu W, Verschraegen CF, Chen L, Mao L, Yeung SC, Kudelka AP, Freedman RS, Kavanagh JJ. Proteomic identification of heat shock protein 70 as a candidate target for enhancing apoptosis induced by farnesyl transferase inhibitor. Proteomics. 2003 Oct;3(10):1904-11. [PubMed]
36. Cho YM, Bae SH, Choi BK, Cho SY, Song CW, Yoo JK, Paik YK. Differential expression of the liver proteome in senescence accelerated mice. Proteomics. 2003 Oct;3(10):1883-94. [PubMed]
37. Borderies G, Jamet E, Lafitte C, Rossignol M, Jauneau A, Boudart G, Monsarrat B, Esquerre-Tugaye MT, Boudet A, Pont-Lezica R. Proteomics of loosely bound cell wall proteins of Arabidopsis thaliana cell suspension cultures: A critical analysis. Electrophoresis. 2003 Oct;24(19-20):3421-32. [PubMed]
38. Sawicki G, Dakour J, Morrish DW. Functional proteomics of neurokinin B in the placenta indicates a novel role in regulating cytotrophoblast antioxidant defences. Proteomics. 2003 Oct;3(10):2044-51. [PubMed]
39. Takahashi N, Yanagida M, Fujiyama S, Hayano T, Isobe T. Proteomic snapshot analyses of preribosomal ribonucleoprotein complexes formed at various stages of ribosome biogenesis in yeast and mammalian cells. Mass Spectrom Rev. 2003 Sep-Oct;22(5):287-317. [PubMed]
40. Xiao GG, Wang M, Li N, Loo JA, Nel AE. Use of proteomics to demonstrate a hierarchical oxidative stress response to diesel exhaust particle chemicals in a macrophage cell line. J Biol Chem. 2003 Sep 30 [Epub ahead of print] [PubMed]
41. Kocks C, Maehr R, Overkleeft HS, Wang EW, Iyer LK, Lennon-Dumenil AM, Ploegh HL, Kessler BM. Functional proteomics of the active cysteine protease content in Drosophila S2 cells. Mol Cell Proteomics. 2003 Sep 16 [Epub ahead of print] [PubMed]
42. Yu YL, Yang PY, Fan HZ, Huang ZY, Rui YC, Yang PY. Protein expressions in macrophage-derived foam cells: comparative analysis by two-dimensional gel electrophoresis. Acta Pharmacol Sin. 2003 Sep;24(9):873-7. [PubMed]
43. Leaner VD, Kinoshita I, Birrer MJ. AP-1 complexes containing cJun and JunB cause cellular transformation of Rat1a fibroblasts and share transcriptional targets. Oncogene. 2003 Aug 28;22(36):5619-29. [PubMed]
44. Huang RY, Boulton SJ, Vidal M, Almo SC, Bresnick AR, Chance MR. High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins. Biochem Biophys Res Commun. 2003 Aug 8;307(4):928-34. [PubMed]
45. Corbin RW, Paliy O, Yang F, Shabanowitz J, Platt M, Lyons CE Jr, Root K, McAuliffe J, Jordan MI, Kustu S, Soupene E, Hunt DF. Toward a protein profile of Escherichia coli: Comparison to its transcription profile. Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9232-7. [PubMed][pdf]
46. Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003 Aug;21(8):921-926. [PubMed][web supplement]
47. Krijgsveld J, Ketting RF, Mahmoudi T, Johansen J, Artal-Sanz M, Verrijzer CP, Plasterk RH, Heck AJ. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol. 2003 Aug;21(8):927-931. [PubMed][web supplement]
    
48. Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E, Hood L, Picone AF, Cherny T, Tjaden BC, Siegel AF, Reilly TJ, Makarova KS, Palsson BO, Smith AL. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol. 2003 Aug;185(15):4593-602. [PubMed]
49. Mo B, Chung Tse Y, Jiang L. Organelle identification and proteomics in plant cells. Trends Biotechnol. 2003 Aug;21(8):331-2.  [PubMed]
50. Liao X, Ying T, Wang H, Wang J, Shi Z, Feng E, Wei K, Wang Y, Zhang X, Huang L, Su G, Huang P. A two-dimensional proteome map of Shigella flexneri. Electrophoresis. 2003 Aug;24(16):2864-82. [PubMed]
51. Nawarak J, Sinchaikul S, Wu CY, Liau MY, Phutrakul S, Chen ST. Proteomics of snake venoms from Elapidae and Viperidae families by multidimensional chromatographic methods. Electrophoresis. 2003 Aug;24(16):2838-54. [PubMed]
52. Bromley E, Leeds N, Clark J, McGregor E, Ward M, Dunn MJ, Tomley F. Defining the protein repertoire of microneme secretory organelles in the apicomplexan parasite Eimeria tenella. Proteomics. 2003 Aug;3(8):1553-61. [PubMed]
53. Krayl M, Benndorf D, Loffhagen N, Babel W. Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert-butyl ether in Pseudomonas putida KT2440. Proteomics. 2003 Aug;3(8):1544-52. [PubMed]
54. Rodriguez-Ortega MJ, Grosvik BE, Rodriguez-Ariza A, Goksoyr A, Lopez-Barea J. Changes in protein expression profiles in bivalve molluscs (Chamaelea gallina) exposed to four model environmental pollutants. Proteomics. 2003 Aug;3(8):1535-43. [PubMed]
55. Madi A, Mikkat S, Ringel B, Ulbrich M, Thiesen HJ, Glocker MO. Mass spectrometric proteome analysis for profiling temperature-dependent changes of protein expression in wild-type Caenorhabditis elegans. Proteomics. 2003 Aug;3(8):1526-34. [PubMed]
56. Froehlich JE, Wilkerson CG, Ray WK, McAndrew RS, Osteryoung KW, Gage DA, Phinney BS. Proteomic study of the Arabidopsis thaliana chloroplastic envelope membrane utilizing alternatives to traditional two-dimensional electrophoresis. J Proteome Res. 2003 Jul-Aug;2(4):413-25. [PubMed]
57. Franzen B, Duvefelt K, Jonsson C, Engelhardt B, Ottervald J, Wickman M, Yang Y, Schuppe-Koistinen I. Gene and protein expression profiling of human cerebral endothelial cells activated with tumor necrosis factor-alpha. Brain Res Mol Brain Res. 2003 Jul 23;115(2):130-46. [PubMed]
58. Wong JH, Balmer Y, Cai N, Tanaka CK, Vensel WH, Hurkman WJ, Buchanan BB. Unraveling thioredoxin-linked metabolic processes of cereal starchy endosperm using proteomics. FEBS Lett. 2003 Jul 17;547(1-3):151-6. [PubMed]
59. Wenk MR, Lucast L, Di Paolo G, Romanelli AJ, Suchy SF, Nussbaum RL, Cline GW, Shulman GI, McMurray W, De Camilli P. Phosphoinositide profiling in complex lipid mixtures using electrospray ionization mass spectrometry. Nat Biotechnol. 2003 Jul;21(7):813-7. [PubMed]
60. Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol. 2003 Jul;13(7):344-56. [PubMed]
61. Pappano WN, Steiglitz BM, Scott IC, Keene DR, Greenspan DS. Use of bmp1/tll1 doubly homozygous null mice and proteomics to identify and validate in vivo substrates of bone morphogenetic protein 1/tolloid-like metalloproteinases. Mol Cell Biol. 2003 Jul;23(13):4428-38. [PubMed]
62. Cooper B, Eckert D, Andon NL, Yates JR, Haynes PA. Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry. J Am Soc Mass Spectrom. 2003 Jul;14(7):736-41. [PubMed]
63. McDonald TG, Van Eyk JE. Mitochondrial proteomics Undercover in the lipid bilayer. Basic Res Cardiol. 2003 Jul;98(4):219-27. [PubMed]
64. Knowles MR, Cervino S, Skynner HA, Hunt SP, De Felipe C, Salim K, Meneses-Lorente G, McAllister G, Guest PC. Multiplex proteomic analysis by two-dimensional differential in-gel electrophoresis. Proteomics. 2003 Jul;3(7):1162-71. [PubMed]
65. Maguire PB, Fitzgerald DJ. Platelet proteomics. J Thromb Haemost. 2003 Jul;1(7):1593-601. [PubMed]

Disease research

1. Zheng Y, Xu Y, Ye B, Lei J, Weinstein MH, O'Leary MP, Richie JP, Mok SC, Liu BC. Prostate carcinoma tissue proteomics for biomarker discovery. Cancer. 2003 Dec 15;98(12):2576-82. [PubMed]
2. Lee CL, Hsiao HH, Lin CW, Wu SP, Huang SY, Wu CY, Wang AH, Khoo KH. Strategic shotgun proteomics approach for efficient construction of an expression map of targeted protein families in hepatoma cell lines. Proteomics. 2003 Dec;3(12):2472-86. [PubMed]
3. Kim CH, Kim do K, Choi SJ, Choi KH, Song KS, Chi J, Koo JS, Hwang SY, Yoon JH, Seong JK. Proteomic and transcriptomic analysis of interleukin-1ss treated lung carcinoma cell line. Proteomics. 2003 Dec;3(12):2454-71. [PubMed]
4. Joo WA, Kang MJ, Son WK, Lee HJ, Lee DY, Lee E, Kim CW. Monitoring protein expression by proteomics: Human plasma exposed to benzene. Proteomics. 2003 Dec;3(12):2402-11. [PubMed]
5. Lorenz P, Bantscheff M, Ibrahim SM, Thiesen HJ, Glocker MO. Proteome analysis of diseased joints from mice suffering from collagen-induced arthritis. Clin Chem Lab Med. 2003 Dec;41(12):1622-32. [PubMed]
6. Ahn WS, Kim KW, Bae SM, Yoon JH, Lee JM, Namkoong SE, Kim JH, Kim CK, Lee YJ, Kim YW. Targeted cellular process profiling approach for uterine leiomyoma using cDNA microarray, proteomics and gene ontology analysis. Int J Exp Pathol. 2003 Dec;84(6):267-279. [PubMed]
7. Garcia A, Prabhakar S, Hughan S, Anderson TW, Brock CJ, Pearce AC, Dwek RA, Watson SP, Hebestreit HF, Zitzmann N. Differential proteome analysis of TRAP-activated platelets: involvement of DOK-2 and phosphorylation of RGS proteins. Blood. 2003 Nov 26 [Epub ahead of print][PubMed]
8. Chen G, Gharib TG, Wang H, Huang CC, Kuick R, Thomas DG, Shedden KA, Misek DE, Taylor JM, Giordano TJ, Kardia SL, Iannettoni MD, Yee J, Hogg PJ, Orringer MB, Hanash SM, Beer DG. Protein profiles associated with survival in lung adenocarcinoma. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13537-42. [PubMed][pdf][web supplement]
9. Sparre T, Bergholdt R, Nerup J, Pociot F. Application of genomics and proteomics in Type 1 diabetes pathogenesis research. Expert Rev Mol Diagn. 2003 Nov;3(6):743-57. [PubMed]
10. Bernard K, Litman E, Fitzpatrick JL, Shellman YG, Argast G, Polvinen K, Everett AD, Fukasawa K, Norris DA, Ahn NG, Resing KA. Functional proteomic analysis of melanoma progression. Cancer Res. 2003 Oct 15;63(20):6716-25. [PubMed]
11. McGregor E, Dunn MJ. Proteomics of heart disease. Hum Mol Genet. 2003 Oct 15;12 Suppl 2:R135-44. [PubMed]
12. Lenz LL, Mohammadi S, Geissler A, Portnoy DA. SecA2-dependent secretion of autolytic enzymes promotes Listeria monocytogenes pathogenesis. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12432-7. [PubMed][pdf]
13. Huber M, Bahr I, Kratzschmar JR, Becker A, Muller EC, Donner P, Pohlenz HD, Schneider MR, Sommer A. Comparison of proteomic and genomic analyses of the human breast cancer cell line T47D and the antiestrogen-resistant derivative T47D-r. Mol Cell Proteomics. 2003 Oct 13 [Epub ahead of print] [PubMed]
14. Marcotte ER, Srivastava LK, Quirion R. cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer's disease. Pharmacol Ther. 2003 Oct;100(1):63-74. [PubMed]
15. Houtman R, Krijgsveld J, Kool M, Romijn EP, Redegeld FA, Nijkamp FP, Heck AJ, Humphery-Smith I. Lung proteome alterations in a mouse model for nonallergic asthma. Proteomics. 2003 Oct;3(10):2008-18. [PubMed]
16. Verma M, Kagan J, Sidransky D, Srivastava S. Proteomic analysis of cancer-cell mitochondria. Nat Rev Cancer. 2003 Oct;3(10):789-95. [PubMed]
17. Somiari RI, Sullivan A, Russell S, Somiari S, Hu H, Jordan R, George A, Katenhusen R, Buchowiecka A, Arciero C, Brzeski H, Hooke J, Shriver C. High-throughput proteomic analysis of human infiltrating ductal carcinoma of the breast. Proteomics. 2003 Oct;3(10):1863-73. [PubMed]
18. Tachibana M, Ohkura Y, Kobayashi Y, Sakamoto H, Tanaka Y, Watanabe J, Amikura K, Nishimura Y, Akagi K. Expression of apolipoprotein A1 in colonic adenocarcinoma. Anticancer Res. 2003 Sep-Oct;23(5b):4161-7. [PubMed]
19. Hiratsuka M, Inoue T, Toda T, Kimura N, Shirayoshi Y, Kamitani H, Watanabe T, Ohama E, Tahimic CG, Kurimasa A, Oshimura M. Proteomics-based identification of differentially expressed genes in human gliomas: down-regulation of SIRT2 gene. Biochem Biophys Res Commun. 2003 Sep 26;309(3):558-66. [PubMed]
20. Jiang M, Jia L, Jiang W, Hu X, Zhou H, Gao X, Lu Z, Zhang Z. Protein disregulation in red blood cell membranes of type 2 diabetic patients. Biochem Biophys Res Commun. 2003 Sep 12;309(1):196-200. [PubMed] 
    
21. Li C, Chen Z, Xiao Z, Wu X, Zhan X, Zhang X, Li M, Li J, Feng X, Liang S, Chen P, Xie J. Comparative proteomics analysis of human lung squamous carcinoma. Biochem Biophys Res Commun. 2003 Sep 12;309(1):253-60. [PubMed]  
22. Turko IV, Murad F. Quantitative protein profiling in heart mitochondria from diabetic rats. J Biol Chem. 2003 Sep 12; [PubMed]
23. Schirmer EC, Florens L, Guan T, Yates JR 3rd, Gerace L. Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science. 2003 Sep 5;301(5638):1380-2. [PubMed][web supplement]
24. Butterfield DA, Boyd-Kimball D, Castegna A. Proteomics in Alzheimer's disease: insights into potential mechanisms of neurodegeneration. J Neurochem. 2003 Sep;86(6):1313-27. [PubMed]
    
25. Ray P, Chen L, Tyurin VA, Kagan VE, Witzmann FA. Proteomic and inducible transgenic approaches to study disease processes. Am J Respir Cell Mol Biol. 2003 Sep;29(3 Suppl):S42-6. [PubMed]
26. Ota J, Yamashita Y, Okawa K, Kisanuki H, Fujiwara S, Ishikawa M, Lim Choi Y, Ueno S, Ohki R, Koinuma K, Wada T, Compton D, Kadoya T, Mano H. Proteomic analysis of hematopoietic stem cell-like fractions in leukemic disorders. Oncogene. 2003 Aug 28;22(36):5720-8. [PubMed]
27. Stierum R, Gaspari M, Dommels Y, Ouatas T, Pluk H, Jespersen S, Vogels J, Verhoeckx K, Groten J, Ommen B. Proteome analysis reveals novel proteins associated with proliferation and differentiation of the colorectal cancer cell line Caco-2. Biochim Biophys Acta. 2003 Aug 21;1650(1-2):73-91. [PubMed]
    
28. Yanagisawa K, Shyr Y, Xu BJ, Massion PP, Larsen PH, White BC, Roberts JR, Edgerton M, Gonzalez A, Nadaf S, Moore JH, Caprioli RM, Carbone DP.  Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet. 2003 Aug 9;362(9382):433-9. [PubMed]
29. Schulenberg B, Beechem JM, Patton WF. Mapping glycosylation changes related to cancer using the Multiplexed Proteomics technology: a protein differential display approach. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Aug 5;793(1):127-39. [PubMed]
30. Powell K. Proteomics delivers on promise of cancer biomarkers. Nat Med. 2003 Aug;9(8):980. [PubMed]
31. Vuadens F, Benay C, Crettaz D, Gallot D, Sapin V, Schneider P, Bienvenut WV, Lemery D, Quadroni M, Dastugue B, Tissot JD. Identification of biologic markers of the premature rupture of fetal membranes: Proteomic approach. Proteomics. 2003 Aug;3(8):1521-5.  [PubMed]
32. Voshol H, Glucksman MJ, van Oostrum J. Proteomics in the discovery of new therapeutic targets for psychiatric disease. Curr Mol Med. 2003 Aug;3(5):447-58. [PubMed]
33. Zheng PP, Luider TM, Pieters R, Avezaat CJ, van den Bent MJ, Sillevis Smitt PA, Kros JM. Identification of tumor-related proteins by proteomic analysis of cerebrospinal fluid from patients with primary brain tumors. J Neuropathol Exp Neurol. 2003 Aug;62(8):855-62. [PubMed]
34. Korc M. Diabetes Mellitus in the era of proteomics. Mol Cell Proteomics. 2003 Jul 7 [Epub ahead of print] [PubMed]
35. Lee KH, Chung HS, Kim HS, Oh SH, Ha MK, Baik JH, Lee S, Bang D. Human alpha-enolase from endothelial cells as a target antigen of anti-endothelial cell antibody in Behcet's disease. Arthritis Rheum. 2003 Jul;48(7):2025-35. [PubMed]
36. Jiang L, Lindpaintner K, Li HF, Gu NF, Langen H, He L, Fountoulakis M. Proteomic analysis of the cerebrospinal fluid of patients with schizophrenia. Amino Acids. 2003 Jul;25(1):49-57. [PubMed]
37. Resing KA. Proteomics for cell protein expression profiling. J Invest Dermatol. 2003 Jul;121(1):XI-XII. [PubMed]
38. Poulaki V. Microdissection, microarrays and proteomics: a new approach to the study of eye diseases. Graefes Arch Clin Exp Ophthalmol. 2003 Jun 26 [Epub ahead of print] [PubMed]
39. Doytchinova IA, Taylor P, Flower DR. Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone. J Biomed Biotechnol. 2003;2003(5):267-290. [PubMed]
40. Fels LM, Buschmann T, Meuer J, Reymond MA, Lamer S, Rocken C, Ebert MP. Proteome analysis for the identification of tumor-associated biomarkers in gastrointestinal cancer. Dig Dis. 2003;21(4):292-8. [PubMed]

Clinical application

1. Clarke W, Zhang Z, Chan DW. The application of clinical proteomics to cancer and other diseases. Clin Chem Lab Med. 2003 Dec;41(12):1562-70. [PubMed]
2. Binz PA, Hochstrasser DF, Appel RD. Mass spectrometry-based proteomics: current status and potential use in clinical chemistry. Clin Chem Lab Med. 2003 Dec;41(12):1540-51. [PubMed]
3. Fusaro VA, Stone JH. Mass spectrometry-based proteomics and analyses of serum: a primer for the clinical investigator. Clin Exp Rheumatol. 2003 Nov-Dec;21(6 Suppl 32):S3-14. [PubMed]
4. Petricoin E 3rd, Liotta LA. Counterpoint: The vision for a new diagnostic paradigm. Clin Chem. 2003 Aug;49(8):1276-8. [PubMed]
5. Diamandis EP. Point: Proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin Chem. 2003 Aug;49(8):1272-5. [PubMed]
6. Banks R, Selby P. Clinical proteomics--insights into pathologies and benefits for patients. Lancet. 2003 Aug 9;362(9382):415-6.  [PubMed]
7. Powell K. Proteomics delivers on promise of cancer biomarkers. Nat Med. 2003 Aug;9(8):980. [PubMed]
8. Angeletti C. Application of proteomic technologies to cytologic specimens. A review. Acta Cytol. 2003 Jul-Aug;47(4):535-44. [PubMed]
9. Dwek MV, Alaiya AA. Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues. Br J Cancer. 2003 Jul 21;89(2):305-7. [PubMed]
10. Petricoin EF, Liotta LA. Clinical Applications of Proteomics. J Nutr. 2003 Jul;133(7):2476S-2484S. [PubMed]
11. Pusch W, Flocco MT, Leung SM, Thiele H, Kostrzewa M. Mass spectrometry-based clinical proteomics. Pharmacogenomics. 2003 Jul;4(4):463-76. [PubMed]
12. Conrads TP, Zhou M, Petricoin EF 3rd, Liotta L, Veenstra TD. Cancer diagnosis using proteomic patterns. Expert Rev Mol Diagn. 2003 Jul;3(4):411-20. [PubMed]

Pharmacogenomics

1. Zheng Y, Xu Y, Ye B, Lei J, Weinstein MH, O'Leary MP, Richie JP, Mok SC, Liu BC. Prostate carcinoma tissue proteomics for biomarker discovery. Cancer. 2003 Dec 15; 98(12): 2576-82. [PubMed]
2. Towbin H, Bair KW, DeCaprio JA, Eck M, Kim S, Kinder FR, Morollo A, Mueller DR, Schindler P, Song HK, Von Oostrum J, Versace RW, Voshol J, Wood J, Zabludoff S, Phillips PE. Proteomics based target identification: Bengamides as a new class of methionine aminopeptidase inhibitors. J Biol Chem. 2003 Oct 8 [Epub ahead of print] [PubMed]
3. Thome-Kromer B, Bonk I, Klatt M, Nebrich G, Taufmann M, Bryant S, Wacker U, Kopke A. Toward the identification of liver toxicity markers: a proteome study in human cell culture and rats. Proteomics. 2003 Oct;3(10):1835-62. [PubMed]
4. Tomer KB, Merrick BA. Toxicoproteomics: a parallel approach to identifying biomarkers. Environ Health Perspect. 2003 Aug;111(11):A578-9. [PubMed]
5. Powell K. Proteomics delivers on promise of cancer biomarkers. Nat Med. 2003 Aug;9(8):980. [PubMed]
6. He QY, Chiu JF. Proteomics in biomarker discovery and drug development. J Cell Biochem. 2003 Aug 1;89(5):868-86.[PubMed]
   

Protein-protein interaction

1. Schulze WX, Mann M. A novel proteomic screen for peptide-protein interactions. J Biol Chem. 2003 Dec 16 [Epub ahead of print] [PubMed]
2. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley Jr RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A Protein Interaction Map of Drosophila melanogaster. Science. 2003 Dec 5;302(5651):1727-1736. [PubMed][Supporting Online Material] 
   
3. Zhong J, Zhang H, Stanyon CA, Tromp G, Finley RL Jr. A Strategy for Constructing Large Protein Interaction Maps Using the Yeast Two-Hybrid System:Regulated Expression Arrays and Two-Phase Mating. Genome Res. 2003 Dec; 13: 2691-2699.[PubMed] [Supplemental Research Data]
4. Grigoriev A. On the number of protein–protein interactions in the yeast proteome. Nucl. Acids. Res. 2003 Jul 15; 31: 4157-4161. [PubMed][pdf]
   

Network/pathway reconstruction and analysis

1. Tornow S, Mewes HW. Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res. 2003 Nov 1;31(21):6283-9. [PubMed]

Structural genomics

1. Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9. [PubMed][PDF]
2. Smith CV, Sacchettini JC. Mycobacterium tuberculosis: a model system for structural genomics. Curr Opin Struct Biol. 2003 Dec;13(6):658-64. [PubMed]
3. Jones DT. Structural biology. Learning to speak the language of proteins. Science. 2003 Nov 21;302(5649):1347-8. [PubMed]
4. Mielke SP, Krishnan VV. Protein structural class identification directly from NMR spectra using averaged chemical shifts. Bioinformatics. 2003 Nov 1;19(16):2054-64.  [PubMed]
5. Hansen C. et al., Microfluidics in structural biology: smaller, faster... better.  Curr Opin Stru Biol. 2003 Oct; [PubMed]
6. Galvao-Botton LM, Katsuyama AM, Guzzo CR, Almeida FC, Farah CS, Valente AP. High-throughput screening of structural proteomics targets using NMR. FEBS Lett. 2003 Sep 25;552(2-3):207-13. [PubMed]
7. Sali A. NIH Workshop on Structural Proteomics of Biological Complexes. Structure (Camb). 2003 Sep;11(9):1043-7. [PubMed]
8. Woestenenk EA, Hammarstrom M, Hard T, Berglund H. Screening methods to determine biophysical properties of proteins in structural genomics.  Anal Biochem. 2003 Jul 1;318(1):71-9. [PubMed]
9. Zolnai Z, Lee PT, Li J, Chapman MR, Newman CS, Phillips GN Jr, Rayment I, Ulrich EL, Volkman BF, Markley JL. Project management system for structural and functional proteomics: Sesame. J Struct Funct Genomics. 2003;4(1):11-23. [PubMed]
10. Kim SH, Shin DH, Choi IG, Schulze-Gahmen U, Chen S, Kim R. Structure-based functional inference in structural genomics. J Struct Funct Genomics. 2003;4(2-3):129-35. [PubMed]
11. Ethier M, Saba JA, Spearman M, Krokhin O, Butler M, Ens W, Standing KG, Perreault H. Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry. Rapid Commun Mass Spectrom. 2003;17(24):2713-20. [PubMed]
12. Deutzmann R. Structural Characterization of Proteins and Peptides. Methods Mol Med. 2003;:269-298. [PubMed]

1. Hsu JL, Huang SY, Chow NH, Chen SH. Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem. 2003 Dec 15;75(24):6843-52. [PubMed]
2. Graumann J, Dunipace LA, Seol JH, McDonald WH, Yates JR 3rd, Wold BJ, Deshaies RJ. Applicability of TAP-MudPIT to pathway proteomics in yeast. Mol Cell Proteomics. 2003 Dec 5 [Epub ahead of print] [PubMed]
3. Zeytun A, Jeromin A, Scalettar BA, Waldo GS, Bradbury AR. Fluorobodies combine GFP fluorescence with the binding characteristics of antibodies. Nat Biotechnol. 2003 Dec;21(12):1473-9. [PubMed]
4. Xiong L, Andrews D, Regnier F. Comparative proteomics of glycoproteins based on lectin selection and isotope coding. J Proteome Res. 2003 Nov-Dec;2(6):618-25. [PubMed]
5. Moon MH, Myung S, Plasencia M, Hilderbrand AE, Clemmer DE. Nanoflow LC/ion mobility/CID/TOF for proteomics: analysis of a human urinary proteome. J Proteome Res. 2003 Nov-Dec;2(6):589-97. [PubMed]
6. Olsen JV, Andersen JR, Nielsen PA, Nielsen ML, Figeys D, Mann M, Wisniewski JR. Hystag - a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain. Mol Cell Proteomics. 2003 Nov 10 [Epub ahead of print] [PubMed]
7. Andrews BJ, Bader GD, Boone C. Playing tag with the yeast proteome. Nat Biotechnol. 2003 Nov;21(11):1297-1299. [PubMed]
8. Wiemann S, Mehrle A, Bechtel S, Wellenreuther R, Pepperkok R, Poustka A; German cDNA Consortium. CDNAs for functional genomics and proteomics: the German Consortium. C R Biol. 2003 Oct-Nov;326(10-11):1003-9. [PubMed]
9. Astorga-Wells J, Jornvall H, Bergman T. A microfluidic electrocapture device in sample preparation for protein analysis by MALDI mass spectrometry. Anal Chem. 2003 Oct 1;75(19):5213-9. [PubMed]
10. Viallet PM, Vo-Dinh T. Monitoring intracellular proteins using fluorescence techniques: from protein synthesis and localization to activity. Curr Protein Pept Sci. 2003 Oct;4(5):375-88. [PubMed]
11. Molloy MP, Brzezinski EE, Hang J, McDowell MT, VanBogelen RA. Overcoming technical variation and biological variation in quantitative proteomics. Proteomics. 2003 Oct;3(10):1912-9. [PubMed]
12. Bertsch M, Kassner RJ. Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel. J Proteome Res. 2003 Sep-Oct;2(5):469-75. [PubMed]
13. Civjan NR, Bayburt TH, Schuler MA, Sligar SG. Direct solubilization of heterologously expressed membrane proteins by incorporation into nanoscale lipid bilayers. Biotechniques. 2003 Sep;35(3):556-60, 562-3. [PubMed]
14. Macht M, Marquardt A, Deininger SO, Damoc E, Kohlmann M, Przybylski M. "Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping. Anal Bioanal Chem. 2003 Aug 30 [Epub ahead of print] [PubMed]
15. Soloviev M, Barry R, Scrivener E, Terrett J. Combinatorial peptidomics: a generic approach for protein expression profiling. J Nanobiotechnology. 2003 Jul 3;1(1):4. [PubMed][pdf]
16. Bradbury A, Velappan N, Verzillo V, Ovecka M, Chasteen L, Sblattero D, Marzari R, Lou J, Siegel R, Pavlik P. Antibodies in proteomics II: screening, high-throughput characterization and downstream applications. Trends Biotechnol. 2003 Jul;21(7):312-7.  [PubMed]
17. Lopez MF, Mikulskis A, Golenko E, Herick K, Spibey CA, Taylor I, Bobrow M, Jackson P. High-content proteomics: Fluorescence multiplexing using an integrated, high-sensitivity, multiwavelength charge-coupled device imaging system. Proteomics. 2003 Jul;3(7):1109-16. [PubMed]
18. Miura K. Imaging technologies for the detection of multiple stains in proteomics. Proteomics. 2003 Jul;3(7):1097-108. [PubMed]
19. Lee SH, Williams MV, DuBois RN, Blair IA. Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry. Rapid Commun Mass Spectrom. 2003;17(19):2168-76. [PubMed]

Protein expression techniques

1. Falk R, Agaton C, Kiesler E, Jin S, Wieslander L, Visa N, Hober S, Stahl S. An improved dual-expression concept, generating high-quality antibodies for proteomics research. Biotechnol Appl Biochem. 2003 Dec;38(Pt 3):231-9. [PubMed]
2. Braun P, LaBaer J. High throughput protein production for functional proteomics. Trends Biotechnol. 2003 Sep;21(9):383-8. [PubMed]
3. Falk R, Agaton C, Kiesler E, Jin S, Wieslander L, Visa N, Hober S, Stahl S. An improved dual expression concept generating high-quality antibodies for proteomics research. Biotechnol Appl Biochem. 2003 Jul 22 [Epub ahead of print] [PubMed]
   

2D gel; Protein purification and chromatographic techniques

1. Watt SA, Patschkowski T, Kalinowski J, Niehaus K. Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT). J Biotechnol. 2003 Dec 19;106(2-3):287-300. [PubMed]
2. Camacho-Carvajal MM, Wollscheid B, Aebersold R, Steimle V, Schamel WW. Two-dimensional Blue Native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates - a proteomics approach. Mol Cell Proteomics. 2003 Dec 9 [Epub ahead of print] [PubMed]
3. Barroso B, Lubda D, Bischoff R. Applications of monolithic silica capillary columns in proteomics. J Proteome Res. 2003 Nov-Dec;2(6):633-42. [PubMed]
4. Shen Y, Tolic N, Masselon C, Pasa-Tolic L, Camp DG 2nd, Lipton MS, Anderson GA, Smith RD. Nanoscale proteomics. Anal Bioanal Chem. 2003 Nov 29 [Epub ahead of print] [PubMed]
5. Terry DE, Desiderio DM. Between-gel reproducibility of the human cerebrospinal fluid proteome. Proteomics. 2003 Oct;3(10):1962-79. [PubMed]
6. Murphy MB, Fuller ST, Richardson PM, Doyle SA. An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res. 2003 Sep 15;31(18):e110. [PubMed]
7. Zhao Y, Zhang W, White MA, Zhao Y. Capillary high-performance liquid chromatography/mass spectrometric analysis of proteins from affinity-purified plasma membrane. Anal Chem. 2003 Aug 1;75(15):3751-7. [PubMed]
8. Zhang W, Zhou G, Zhao Y, White MA, Zhao Y. Affinity enrichment of plasma membrane for proteomics analysis. Electrophoresis. 2003 Aug;24(16):2855-63. [PubMed]
9. Scheich C, Sievert V, Bussow K. An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography. BMC Biotechnol. 2003 Jul 28 [Epub ahead of print] [PubMed]
10. Mark Smales C, Birch JR, Racher AJ, Marshall CT, James DC. Evaluation of individual protein errors in silver-stained two-dimensional gels. Biochem Biophys Res Commun. 2003 Jul 11;306(4):1050-5. [PubMed]
11. Wang W, Scali M, Vignani R, Spadafora A, Sensi E, Mazzuca S, Cresti M. Protein extraction for two-dimensional electrophoresis from olive leaf, a plant tissue containing high levels of interfering compounds. Electrophoresis. 2003 Jul;24(14):2369-75. [PubMed]
12. Shang TQ, Ginter JM, Johnston MV, Larsen BS, McEwen CN. Carrier ampholyte-free solution isoelectric focusing as a prefractionation method for the proteomic analysis of complex protein mixtures. Electrophoresis. 2003 Jul;24(14):2359-68. [PubMed]
13. Lolli G, Thaler F, Valsasina B, Roletto F, Knapp S, Uggeri M, Bachi A, Matafora V, Storici P, Stewart A, Kalisz HM, Isacchi A. Inhibitor affinity chromatography: Profiling the specific reactivity of the proteome with immobilized molecules. Proteomics. 2003 Jul;3(7):1287-98. [PubMed]
14. Iyer S, Olivares J. Trypsin digestion of proteins on intact immobilized pH gradient strips for surface matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis. Rapid Commun Mass Spectrom. 2003;17(20):2323-6. [PubMed]

Mass spectrometry

1. Watt SA, Patschkowski T, Kalinowski J, Niehaus K. Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT). J Biotechnol. 2003 Dec 19;106(2-3):287-300. [PubMed]
2. Moyer SC, Budnik BA, Pittman JL, Costello CE, O'Connor PB. Attomole Peptide analysis by high-pressure matrix-assisted laser desorption/ionization fourier transform mass spectrometry. Anal Chem. 2003 Dec 1;75(23):6449-54. [PubMed]
3. Yaneva M, Tempst P. Affinity Capture of Specific DNA-Binding Proteins for Mass Spectrometric Identification. Anal Chem. 2003 Dec 1;75(23):6437-48. [PubMed]
4. Michalet S, Favreau P, Stocklin R. Profiling and in vivo quantification of proteins by high resolution mass spectrometry: the example of goserelin, an analogue of luteinizing hormone-releasing hormone. Clin Chem Lab Med. 2003 Dec;41(12):1589-98. [PubMed]
5. Shen Y, Tolic N, Masselon C, Pasa-Tolic L, Camp DG 2nd, Lipton MS, Anderson GA, Smith RD. Nanoscale proteomics. Anal Bioanal Chem. 2003 Nov 29 [Epub ahead of print] [PubMed]
6. Baldwin MA. Protein Identification by Mass Spectrometry: Issues to be Considered. Mol Cell Proteomics. 2003 Nov 6 [Epub ahead of print] [PubMed]
7. Myung S, Lee YJ, Moon MH, Taraszka J, Sowell R, Koeniger S, Hilderbrand AE, Valentine SJ, Cherbas L, Cherbas P, Kaufmann TC, Miller DF, Mechref Y, Novotny MV, Ewing MA, Sporleder CR, Clemmer DE. Development of high-sensitivity ion trap ion mobility spectrometry time-of-flight techniques: a high-throughput nano-LC-IMS-TOF separation of peptides arising from a Drosophila protein extract. Anal Chem. 2003 Oct 1;75(19):5137-45.  [PubMed]
8. Emmett MR. Determination of post-translational modifications of proteins by high-sensitivity, high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J Chromatogr A. 2003 Sep 26;1013(1-2):203-13. [PubMed]
9. Sanz-Medel A, Montes-Bayon M, Luisa Fernandez Sanchez M. Trace element speciation by ICP-MS in large biomolecules and its potential for proteomics. Anal Bioanal Chem. 2003 Aug 5 [Epub ahead of print] [PubMed]  
   
10. Brock A, Horn DM, Peters EC, Shaw CM, Ericson C, Phung QT, Salomon AR. An automated matrix-assisted laser desorption/ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometer for "bottom-up" proteomics. Anal Chem. 2003 Jul 15;75(14):3087-96. [PubMed]
11. Nepomuceno AI, Muddiman DC, Bergen HR 3rd, Craighead JR, Burke MJ, Caskey PE, Allan JA. Dual electrospray ionization source for confident generation of accurate mass tags using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem. 2003 Jul 15;75(14):3079-86. [PubMed]
12. Villanueva J, Yanes O, Querol E, Serrano L, Aviles FX. Identification of protein ligands in complex biological samples using intensity-fading MALDI-TOF mass spectrometry. Anal Chem. 2003 Jul 15;75(14):3053-63. [PubMed]
13. Aebersold R. A mass spectrometric journey into protein and proteome research. J Am Soc Mass Spectrom. 2003 Jul;14(7):685-95. [PubMed]
14. Heller M, Mattou H, Menzel C, Yao X. Trypsin catalyzed (16)O-to-(18)O exchange for comparative proteomics: tandem mass spectrometry comparison using MALDI-TOF, ESI-QTOF, and ESI-ion trap mass spectrometers. J Am Soc Mass Spectrom. 2003 Jul;14(7):704-18. [PubMed]
    

Protein-protein interaction study

1. Zhong J, Zhang H, Stanyon CA, Tromp G, Finley RL Jr. A Strategy for Constructing Large Protein Interaction Maps Using the Yeast Two-Hybrid System:Regulated Expression Arrays and Two-Phase Mating. Genome Res. 2003 Dec; 13: 2691-2699.[PubMed] [Supplemental Research Data]
2. Yan Y, Marriott G. Analysis of protein interactions using fluorescence technologies. Curr Opin Chem Biol. 2003 Oct;7(5):635-40. [PubMed]
3. Mackun K, Downard KM. Strategy for identifying protein–protein interactions of gel-separated proteins and complexes by mass spectrometry. Anal Biochem. 2003 Jul 1;318(1):60-70. [PubMed]
   

Protein function study

1. Liebel U, Starkuviene V, Erfle H, Simpson JC, Poustka A, Wiemann S, Pepperkok R. A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Lett. 2003 Nov 20;554(3):394-8. [PubMed]
   

Post-translational modification study

1. Ibarrola N, Kalume DE, Gronborg M, Iwahori A, Pandey A. A Proteomic Approach for Quantitation of Phosphorylation Using Stable Isotope Labeling in Cell Culture. Anal Chem. 2003 Nov 15;75(22):6043-6049. [PubMed]
2. Emmett MR. Determination of post-translational modifications of proteins by high-sensitivity, high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J Chromatogr A. 2003 Sep 26;1013(1-2):203-13. [PubMed]
3. Ghezzi P, Bonetto V. Redox proteomics: Identification of oxidatively modified proteins. Proteomics. 2003 Jul;3(7):1145-53. [PubMed]
4. Steinberg TH, Agnew BJ, Gee KR, Leung WY, Goodman T, Schulenberg B, Hendrickson J, Beechem JM, Haugland RP, Patton WF. Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology. Proteomics. 2003 Jul;3(7):1128-44. [PubMed]
   

Data analysis

1. Wilke A, Ruckert C, Bartels D, Dondrup M, Goesmann A, Huser AT, Kespohl S, Linke B, Mahne M, McHardy A, Puhler A, Meyer F. Bioinformatics support for high-throughput proteomics. J Biotechnol. 2003 Dec 19;106(2-3):147-56. [PubMed]
2. MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR 3rd. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem. 2003 Dec 15;75(24):6912-21. [PubMed]
3. Zhu W, Wang X, Ma Y, Rao M, Glimm J, Kovach JS. Detection of cancer-specific markers amid massive mass spectral data. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14666-14671. [PubMed][pdf]
4. Kwon KH, Kim M, Kim JY, Kim KW, Kim SI, Park YM, Yoo JS. Efficiency improvement of peptide identification for an organism without complete genome sequence, using expressed sequence tag database and tandem mass spectral data. Proteomics. 2003 Dec;3(12):2305-9. [PubMed]
5. Mielke SP, Krishnan VV. Protein structural class identification directly from NMR spectra using averaged chemical shifts. Bioinformatics. 2003 Nov 1;19(16):2054-64.  [PubMed]
6. Lu B, Chen T. A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Bioinformatics. 2003 Oct;19 Suppl 2:II113-II121. [PubMed]
7. Orchard S, Zhu W, Julian RK Jr, Hermjakob H, Apweiler R. Further advances in the development of a data interchange standard for proteomics data. Proteomics. 2003 Oct;3(10):2065-6. [PubMed]
8. Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics. 2003 Sep 1;19(13):1636-1643. [PubMed]
9. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003 Sep 1;75(17):4646-58. [PubMed]
10. Malmodin D, Papavoine CH, Billeter M. Fully automated sequence-specific resonance assignments of hetero- nuclear protein spectra. J Biomol NMR. 2003 Sep;27(1):69-79. [PubMed]
11. Laugesen S, Roepstorff P. Combination of two matrices results in improved performance of maldi ms for peptide mass mapping and protein analysis. J Am Soc Mass Spectrom. 2003 Sep;14(9):992-1002. [PubMed]
12. Henzel WJ, Watanabe C, Stults JT. Protein identification: the origins of peptide mass fingerprinting. J Am Soc Mass Spectrom. 2003 Sep;14(9):931-42. [PubMed]
13. Purohit PV, Rocke DM. Discriminant models for high-throughput proteomics mass spectrometer data. Proteomics. 2003 Sep;3(9):1699-703. [PubMed]
14. Lee KR, Lin X, Park DC, Eslava S. Megavariate data analysis of mass spectrometric proteomics data using latent variable projection method. Proteomics. 2003 Sep;3(9):1680-6. [PubMed]    
15. Baggerly KA, Morris JS, Wang J, Gold D, Xiao LC, Coombes KR. A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics. 2003 Sep;3(9):1667-72. [PubMed]  
16. Cagney G, Amiri S, Premawaradena T, Lindo M, Emili A. In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci. 2003 Aug 13;1(1):5. [PubMed][pdf]
17. Somorjai RL, Dolenko B, Baumgartner R. Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. Bioinformatics. 2003 Aug 12;19(12):1484-91. [PubMed]
18. Colinge J, Masselot A, Giron M, Dessingy T, Magnin J. OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics. 2003 Aug;3(8):1454-63. [PubMed]
19. Colinge J, Magnin J, Dessingy T, Giron M, Masselot A. Improved peptide charge state assignment. Proteomics. 2003 Aug;3(8):1434-40. [PubMed]
20. Dowsey AW, Dunn MJ, Yang GZ. The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics. 2003 Aug;3(8):1567-96. [PubMed]
21. Marengo E, Leardi R, Robotti E, Righetti PG, Antonucci F, Cecconi D. Application of three-way principal component analysis to the evaluation of two-dimensional maps in proteomics. J Proteome Res. 2003 Jul-Aug;2(4):351-60. [PubMed]
22. Chamrad DC, Koerting G, Gobom J, Thiele H, Klose J, Meyer HE, Blueggel M. Interpretation of mass spectrometry data for high-throughput proteomics. Anal Bioanal Chem. 2003 Jul 5 [Epub ahead of print] [PubMed]
23. Yasui Y, Pepe M, Thompson ML, Adam BL, Wright GL Jr, Qu Y, Potter JD, Winget M, Thornquist M, Feng Z. A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatistics. 2003 Jul;4(3):449-63. [PubMed]
24. Ethier M, Saba JA, Spearman M, Krokhin O, Butler M, Ens W, Standing KG, Perreault H. Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry. Rapid Commun Mass Spectrom. 2003;17(24):2713-20. [PubMed]

Software

1. Martinez-Cruz LA, Rubio A, Martinez-Chantar ML, Labarga A, Barrio I, Podhorski A, Segura V, Sevilla Campo JL, Avila MA, Mato JM. GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data. Bioinformatics. 2003 Nov 1;19(16):2158-60.  [PubMed]
2. Lundgren DH, Eng J, Wright ME, Han DK. PROTEOME-3D: An interactive bioinformatics tool for large-scale data exploration and knowledge discovery. Mol Cell Proteomics. 2003 Sep 7 [Epub ahead of print] [PubMed]
   

Database

1. Hill A, Kim H. The UAB Proteomics Database. Bioinformatics. 2003 Nov 1;19(16):2149-51.  [PubMed]
2. Henrick K, Newman R, Tagari M, Chagoyen M. EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J Struct Biol. 2003 Oct;144(1-2):228-37. [PubMed]
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