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

General Nature Insight Proteomics 2003 Mar 13; 422 Expression profiling    2-dimensional (2D) gel electrophoresis    2-dimensional (2D) gel electrophoresis & mass spectrometry (MS)    Liquid chromatography (LC) & mass spectrometry (MS)    Other approaches Protein-protein interaction    Network/pathway reconstruction and analysis Application    Disease research    Clinical application    Pharmacogenomics 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. Figeys D. Proteomics in 2002: a year of technical development and wide-ranging applications. Anal Chem. 2003 Jun 15;75(12):2891-905. [PubMed]
2. Molloy MP. The challenge of industrializing proteomics. Nat Biotechnol. 2003 Jun;21(6):597. [PubMed]
3. Gillespie M. Affordable proteomics: the two-hybrid systems. Curr Opin Mol Ther. 2003 Jun;5(3):266-70. [PubMed]
4. Apweiler R, Martin MJ, O'Donovan C, Pruess M. Managing core resources for genomics and proteomics. Pharmacogenomics. 2003 May;4(3):343-50. [PubMed]
5. Merrick BA. The Human Proteome Organization (HUPO) and Environmental Health. Environ Health Perspect. 2003 May;111(6):797-801. [PubMed]
6. Sawyer TK, Chorev M. Peptide revolution: genomics, proteomics and therapeutics. Biotechniques. 2003 Mar;34(3):594-6, 598-9. [PubMed]
7. Patterson SD, Aebersold RH. Proteomics: the first decade and beyond. Nat Genet. 2003 Mar;33 Suppl:311-23. [PubMed]
   
8. A cast of thousands. Nat Biotechnol. 2003 Mar;21(3):213. [PubMed]
9. Mitchell P. In the pursuit of industrial proteomics. Nat Biotechnol. 2003 Mar;21(3):233-7. [PubMed]
10. Huber LA. Opinion: Is proteomics heading in the wrong direction? Nat Rev Mol Cell Biol. 2003 Jan;4(1):74-80. [PubMed]
11. Merrick BA. The human proteome organization (HUPO) and environmental health. EHP Toxicogenomics. 2003 Jan;111(1T):1-5. [PubMed]
12. Mouledous L, Gutstein HB. Gene arrays and proteomics. A primer. Methods Mol Med. 2003;84:141-54. [PubMed]
13. Benner SA. Interpretive proteomics-finding biological meaning in genome and proteome databases. Adv Enzyme Regul. 2003;43:271-359. [PubMed]
14. Morrison RS, Kinoshita Y, Johnson MD, Conrads TP. Proteomics in the postgenomic age. Adv Protein Chem. 2003;65:1-23. [PubMed]
15. Zhu H, Bilgin M, Snyder M. Proteomics. Annu Rev Biochem. 2003;72:783-812. [PubMed]

1. Marte B. proteomics. Nature. 2003 Mar 13;422(6928):191. [PubMed]
2. Tyers M, Mann M. From genomics to proteomics. Nature. 2003 Mar 13;422(6928):193-7. [PubMed]
3. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003 Mar 13;422(6928):198-207. [PubMed]
4. Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature. 2003 Mar 13;422(6928):208-15. [PubMed]
5. Sali A, Glaeser R, Earnest T, Baumeister W. From words to literature in structural proteomics. Nature. 2003 Mar 13;422(6928):216-25.  [PubMed]
6. Hanash S. Disease proteomics. Nature. 2003 Mar 13;422(6928):226-32.  [PubMed]
7. Boguski MS, McIntosh MW. Biomedical informatics for proteomics. Nature. 2003 Mar 13;422(6928):233-7.  [PubMed]

Expression profiling

2-dimensional (2D) gel electrophoresis

1. Chen W, Ji J, Xu X, He S, Ru B. Proteomic comparison between human young and old brains by two-dimensional gel electrophoresis and identification of proteins. Int J Dev Neurosci. 2003 Jun;21(4):209-16. [PubMed]
2. Krapfenbauer K, Fountoulakis M, Lubec G. A rat brain protein expression map including cytosolic and enriched mitochondrial and microsomal fractions. Electrophoresis. 2003 Jun;24(11):1847-70. [PubMed]
3. Gongora R, Acestor N, Quadroni M, Fasel N, Saravia NG, Walker J. Mapping the proteome of Leishmania Viannia parasites using two-dimensional polyacrylamide gel electrophoresis and associated technologies. Biomedica. 2003 Jun;23(2):153-60. [PubMed]
4. Shen S, Jing Y, Kuang T. Proteomics approach to identify wound-response related proteins from rice leaf sheath. Proteomics. 2003 Apr;3(4):527-35. [PubMed]
5. Weekes J, Watson RR, Dunn MJ. Murine retrovirus infection and the effect of chronic alcohol consumption: proteomic analysis of cardiac protein expression. Alcohol Alcohol. 2003 Mar-Apr;38(2):103-8. [PubMed]
6. Heijne WH, Stierum RH, Slijper M, van Bladeren PJ, van Ommen B. Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach. Biochem Pharmacol. 2003 Mar 1;65(5):857-75. [PubMed]
7. Riedel K, Arevalo-Ferro C, Reil G, Gorg A, Lottspeich F, Eberl L. Analysis of the quorum-sensing regulon of the opportunistic pathogen Burkholderia cepacia H111 by proteomics. Electrophoresis. 2003 Feb;24(4):740-50. [PubMed]
8. Komatsu S, Konishi H, Shen S, Yang G. Rice proteomics: a step toward functional analysis of the rice genome. Mol Cell Proteomics. 2003 Jan;2(1):2-10. [PubMed]

2-dimensional (2D) gel electrophoresis & mass spectrometry (MS)

1. Van Den Bergh G, Clerens S, Cnops L, Vandesande F, Arckens L. Fluorescent two-dimensional difference gel electrophoresis and mass spectrometry identify age-related protein expression differences for the primary visual cortex of kitten and adult cat. J Neurochem. 2003 Apr;85(1):193-205. [PubMed]
2. Edvardsson U, Brockenhuus Von Lowenhielm H, Panfilov O, Nystrom AC, Nilsson F, Dahllof B. Hepatic protein expression of lean mice and obese diabetic mice treated with peroxisome proliferator-activated receptor activators. Proteomics. 2003 Apr;3(4):468-78. [PubMed]
3. Santamaria E, Avila MA, Latasa MU, Rubio A, Martin-Duce A, Lu SC, Mato JM, Corrales FJ. Functional proteomics of nonalcoholic steatohepatitis: Mitochondrial proteins as targets of S-adenosylmethionine. Proc Natl Acad Sci U S A 2003 Mar 18;100(6):3065-70 [PubMed]
4. You SA, Archacki SR, Angheloiu G, Moravec CS, Rao S, Kinter M, Topol EJ, Wang Q. Proteomic approach to coronary atherosclerosis shows ferritin light chain as a significant marker: evidence consistent with iron hypothesis in atherosclerosis. Physiol Genomics. 2003 Mar 18;13(1):25-30. [PubMed]
5. Paulson L, Martin P, Persson A, Nilsson CL, Ljung E, Westman-Brinkmalm A, Eriksson PS, Blennow K, Davidsson P. Comparative genome- and proteome analysis of cerebral cortex from MK-801-treated rats. J Neurosci Res. 2003 Feb 15;71(4):526-33. [PubMed]
6. Bernhardt J, Weibezahn J, Scharf C, Hecker M. Bacillus subtilis During Feast and Famine: Visualization of the Overall Regulation of Protein Synthesis During Glucose Starvation by Proteome Analysis. Genome Res. 2003 Feb;13(2):224-37. [PubMed]
7. Van Dyk DD, Misztal DR, Wilkins MR, Mackintosh JA, Poljak A, Varnai JC, Teber E, Walsh BJ, Gray PP. Identification of cellular changes associated with increased production of human growth hormone in a recombinant Chinese hamster ovary cell line. Proteomics. 2003 Feb;3(2):147-156. [PubMed]
8. Gromov P, Skovgaard GL, Palsdottir H, Gromova I, Ostergaard M, Celis JE.  Protein profiling of the human epidermis from the elderly reveals Up regulation of a signature of INF-gamma induced polypeptides that includes MnSOD and PI3K. Mol Cell Proteomics. 2003 Jan 17 [epub ahead of print] [PubMed]
9. Fountoulakis M, Schlaeger EJ. The mitochondrial proteins of the neuroblastoma cell line IMR-32. Electrophoresis. 2003 Jan;24(1-2):260-75. [PubMed] 
   

Liquid chromatography (LC) & mass spectrometry (MS);

1. Salomon AR, Ficarro SB, Brill LM, Brinker A, Phung QT, Ericson C, Sauer K, Brock A, Horn DM, Schultz PG, Peters EC. Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc Natl Acad Sci U S A. 2003 Jan 21;100(2):443-448. [PubMed]
2. Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ. Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond). 2003 Jan 15 [epub ahead of print] [PubMed]
3. Zolla L, Timperio AM, Walcher W, Huber CG. Proteomics of Light-Harvesting Proteins in Different Plant Species. Analysis and Comparison by Liquid Chromatography-Electrospray Ionization Mass Spectrometry. Photosystem II. Plant Physiol. 2003 Jan;131(1):198-214. [PubMed]
   

Other approaches

1. Agaton C, Galli J, Hoiden Guthenberg I, Janzon L, Hansson M, Asplund A, Brundell E, Lindberg S, Ruthberg I, Wester K, Wurtz D, Hoog C, Lundeberg J, Stahl S, Ponten F, Uhlen M. Affinity Proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol Cell Proteomics. 2003 Jun 9 [Epub ahead of print] [PubMed]
2. Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A. PRISM: A generic large-scale proteomics investigation strategy for mammals. Mol Cell Proteomics. 2003 Feb 10 [epub ahead of print] [PubMed]
3. Jensen KB, Jensen ON, Ravn P, Clark BF, Kristensen P. Identification of keratinocyte specific markers using phage display and mass spectrometry. Mol Cell Proteomics. 2003 Jan 17 [epub ahead of print] [PubMed]
4. Balmer Y, Koller A, Del Val G, Manieri W, Schurmann P, Buchanan BB. Proteomics gives insight into the regulatory function of chloroplast thioredoxins. Proc Natl Acad Sci U S A 2003 Jan 7;100(1):370-375 [PubMed][pdf]

1. Suzuki H, Saito R, Kanamori M, Kai C, Schonbach C, Nagashima T, Hosaka J, Hayashizaki Y. The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer. Genome Res. 2003 Jun;13(6B):1534-41. [PubMed][pdf]
2. Lu L, Arakaki AK, Lu H, Skolnick J. Multimeric Threading-Based Prediction of Protein-Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome. Genome Res. 2003 Jun;13(6):1146-54. [PubMed][pdf]
3. Salwinski L. et al., Computational methods of analysis of protein–protein interactions. Curr Opin Struct Biol. 2003 Jun; [PubMed]
4. Janin J. et al., Genome-wide studies of protein–protein interaction. Curr Opin Struct Biol. 2003 Jun; [PubMed]
5. Saito R, Suzuki H, Hayashizaki Y. Construction of reliable protein-protein interaction networks with a new interaction generality measure. Bioinformatics. 2003 Apr 12;19(6):756-63. [PubMed]
6. Sprinzak E, Sattath S, Margalit H. How Reliable are Experimental Protein–Protein Interaction Data? J Mol Biol. 2003 Apr 11; 327:919-923. [PubMed]
7. Drewes G, Bouwmeester T. Global approaches to protein–protein interactions. Curr Opin Cell Biol. 2003 Apr; 15:199-205. [PubMed]
8. Huynen MA, Snel B, Mering C, Bork P. Function prediction and protein networks. Curr Opin Cell Biol. 2003 Apr; 15:191-198. [PubMed]
9. Archakov AI, Govorun VM, Dubanov AV, Ivanov YD, Veselovsky AV, Lewi P, Janssen P. Protein-protein interactions as a target for drugs in proteomics. Proteomics. 2003 Apr;3(4):380-91. [PubMed]
   
10. Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol. 2003 Mar;21(3):315-8. [PubMed][web supplement]
11. Sidhu SS, Bader GD, Boone C.  Functional genomics of intracellular peptide recognition domains with combinatorial biology methods. Curr Opin Chem Biol. 2003 Feb; 7: 97-102. [PubMed]
12. Yuryev A, Wennogle LP. Novel raf kinase protein-protein interactions found by an exhaustive yeast two-hybrid analysis. Genomics. 2003 Feb;81(2):112-25. [PubMed]
13. Bock JR, Gough DA. Whole-proteome interaction mining. Bioinformatics. 2003 Jan;19(1):125-134. [PubMed]
14. Ju BH, Park B, Park JH, Han K. Visualization and analysis of protein interactions. Bioinformatics. 2003 Jan;19(2):317-8. [PubMed]
15. Coates P, Hall P. The yeast two-hybrid system for identifying protein-protein interactions. J Pathol. 2003 Jan;199(1):4-7. [PubMed]

Network/pathway reconstruction and analysis

1. Huynen MA, Snel B, Mering C, Bork P. Function prediction and protein networks. Curr Opin Cell Biol. 2003 Apr;15(2):191-8. [PubMed]

Application

1. Castegna A, Thongboonkerd V, Klein JB, Lynn B, Markesbery WR, Butterfield DA. Proteomic identification of nitrated proteins in Alzheimer's disease brain. J Neurochem. 2003 Jun;85(6):1394-1401. [PubMed]
2. Djordjevic MA, Chen HC, Natera S, Van Noorden G, Menzel C, Taylor S, Renard C, Geiger O, Weiller GF; Sinorhizobium DNA Sequencing Consortium. A global analysis of protein expression profiles in Sinorhizobium meliloti: discovery of new genes for nodule occupancy and stress adaptation. Mol Plant Microbe Interact. 2003 Jun;16(6):508-24. [PubMed]
3. Kinoshita K, Nakamura H. Protein informatics towards function identification. Curr Opin Struct Biol. 2003 Jun;13(3):396-400. [PubMed]
4. Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schonbach C, Teasdale RD, Yuan Z. Mouse Proteome Analysis. Genome Res. 2003 Jun;13(6B):1335-44.  [PubMed][pdf]
5. Semple CA. The comparative proteomics of ubiquitination in mouse. Genome Res. 2003 Jun;13(6B):1389-94. [PubMed]
6. Admon A, Barnea E, Ziv T. Tumor antigens and proteomics from the point of view of the major histocompatibility complex peptides. Mol Cell Proteomics. 2003 Jun 23 [Epub ahead of print] [PubMed]
7. Godovac-Zimmermann J, Brown LR. Proteomics approaches to elucidation of signal transduction pathways. Curr Opin Mol Ther. 2003 Jun;5(3):241-9. [PubMed]
8. Kim E, Park JM. Identification of Novel Target Proteins of Cyclic GMP Signaling Pathways Using Chemical Proteomics. J Biochem Mol Biol. 2003 May 31;36(3):299-304. [PubMed]
9. Prabhakar N, Champagnat J. Functional genomics and proteomics in control of breathing. Respir Physiol Neurobiol. 2003 May 30;135(2-3):107-8. [PubMed]
10. Gaston B. Functional genomics and proteomics in control of breathing. Respir Physiol Neurobiol. 2003 May 30;135(2-3):231-8. [PubMed]
11. Rojo E, Zouhar J, Carter C, Kovaleva V, Raikhel NV. A unique mechanism for protein processing and degradation in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2003 May 28 [Epub ahead of print] [PubMed][pdf]
12. Ferro M, Salvi D, Brugiere S, Miras S, Kowalski S, Louwagie M, Garin J, Joyard J, Rolland N. Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana. Mol Cell Proteomics. 2003 May 28 [Epub ahead of print] [PubMed]
13. Huber LA, Pfaller K, Vietor I. Organelle proteomics: implications for subcellular fractionation in proteomics. Circ Res. 2003 May 16;92(9):962-8. [PubMed]
14. Zaia J, Costello CE. Tandem mass spectrometry of sulfated heparin-like glycosaminoglycan oligosaccharides. Anal Chem. 2003 May 15;75(10):2445-55. [PubMed]
15. Kjeldsen F, Haselmann KF, Budnik BA, Sorensen ES, Zubarev RA. Complete characterization of posttranslational modification sites in the bovine milk protein PP3 by tandem mass spectrometry with electron capture dissociation as the last stage. Anal Chem. 2003 May 15;75(10):2355-61. [PubMed]
16. Foster LJ, De Hoog CL, Mann M. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A 2003 May 13;100(10):5813-8 [PubMed][pdf][web supplement]
17. Tryoen-Toth P, Richert S, Sohm B, Mine M, Marsac C, Van Dorsselaer A, Leize E, Florentz C. Proteomic consequences of a human mitochondrial tRNA mutation beyond the frame of mitochondrial translation. J Biol Chem. 2003 Apr 24 [epub ahead of print] [PubMed]
18. Ashcroft AE. Protein and peptide identification: the role of mass spectrometry in proteomics. Nat Prod Rep. 2003 Apr;20(2):202-15. [PubMed]
19. Huynen MA, Snel B, Mering C, Bork P. Function prediction and protein networks. Curr Opin Cell Biol. 2003 Apr;15(2):191-8. [PubMed]
20. Pang JX, Ginanni N, Dongre AR, Hefta SA, Opitek GJ. Biomarker discovery in urine by proteomics. J Proteome Res. 2002 Mar-Apr;1(2):161-9. [PubMed]
21. Bandara LR, Kelly MD, Lock EA, Kennedy S. A Correlation between a Proteomic Evaluation and Conventional Measurements in the Assessment of Renal Proximal Tubular Toxicity. Toxicol Sci. 2003 Mar 25 [epub ahead of print] [PubMed]
22. Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates JR 3rd. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3107-3112. [PubMed][pdf][web supplement]
23. Islam N, Tsujimoto H, Hirano H. Wheat proteomics: Relationship between fine chromosome deletion and protein expression. Proteomics. 2003 Mar;3(3):307-16. [PubMed]
24. Wu CC, Yates JR. The application of mass spectrometry to membrane proteomics. Nat Biotechnol. 2003 Mar;21(3):262-7. [PubMed]
25. Westermann B, Neupert W. 'Omics' of the mitochondrion. Nat Biotechnol. 2003 Mar;21(3):239-40. [PubMed]
26. Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS. Characterization of the human heart mitochondrial proteome. Nat Biotechnol. 2003 Mar;21(3):281-6. [PubMed][web supplement]
27. Ozawa T, Sako Y, Sato M, Kitamura T, Umezawa Y. A genetic approach to identifying mitochondrial proteins. Nat Biotechnol. 2003 Mar;21(3):287-93. [PubMed][web supplement]
28. Yatsuda AP, Krijgsveld J, Cornelissen AW, Heck AJ, De Vries E. Comprehensive analysis of the secreted proteins of the parasite Haemonchus contortus reveals extensive sequence variation and differential immune recognition. J Biol Chem. 2003 Feb 7 [epub ahead of print] [PubMed]
29. Gavin AC, Superti-Furga G. Protein complexes and proteome organization from yeast cell. Curr Opin Chem Biol.2003 Feb; 7:21-27. [PubMed]
30. Millar AH, Heazlewood JL. Genomic and proteomic analysis of mitochondrial carrier proteins in Arabidopsis. Plant Physiol. 2003 Feb;131(2):443-53. [PubMed]
31. Lubec G, Krapfenbauer K, Fountoulakis M. Proteomics in brain research: potentials and limitations. Prog Neurobiol. 2003 Feb;69(3):193-211. [PubMed]
32. Dreger M. Subcellular proteomics. Mass Spectrom Rev. 2003 Feb;22(1):27-56. [PubMed]
33. Mootha VK, Lepage P, Miller K, Bunkenborg J, Reich M, Hjerrild M, Delmonte T, Villeneuve A, Sladek R, Xu F, Mitchell GA, Morin C, Mann M, Hudson TJ, Robinson B, Rioux JD, Lander ES. Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A 2003 Jan 21;100(2):605-610 [PubMed][pdf]
34. Liska AJ, Shevchenko A. Expanding the organismal scope of proteomics: Cross-species protein identification by mass spectrometry and its implications. Proteomics. 2003 Jan;3(1):19-28. [PubMed]
35. Higai K, Shibukawa K, Muto S, Matsumoto K. Targeted proteo-glycomics analysis of Sialyl Lewis X antigen expressing glycoproteins secreted by human hepatoma cell line. Anal Sci. 2003 Jan;19(1):85-92. [PubMed]
36. Nouwens AS, Walsh BJ, Cordwell SJ. Application of proteomics to Pseudomonas aeruginosa. Adv Biochem Eng Biotechnol. 2003;83:117-40. [PubMed]
37. Cash P. Proteomics of bacterial pathogens. Adv Biochem Eng Biotechnol. 2003;83:93-115. [PubMed]
38. Hecker M. A proteomic view of cell physiology of Bacillus subtilis--bringing the genome sequence to life. Adv Biochem Eng Biotechnol. 2003;83:57-92. [PubMed]
39. VanBogelen RA. Probing the molecular physiology of the microbial organism, Escherichia coli using proteomics. Adv Biochem Eng Biotechnol. 2003;83:27-55. [PubMed]
40. Mullner S. The impact of proteomics on products and processes. Adv Biochem Eng Biotechnol. 2003;83:1-25. [PubMed]
41. Whitelegge JP, Gomez SM, Faull KF. Proteomics of membrane proteins. Adv Protein Chem. 2003;65:271-307. [PubMed]
42. Conrads TP, Issaq HJ, Hoang VM. Current strategies for quantitative proteomics. Adv Protein Chem. 2003;65:133-59. [PubMed]
43. Haseloff RF, Krause E, Blasig IE. Proteomics of Brain Endothelium: Separation of Proteins by Two-Dimensional Gel Electrophoresis and Identification by Mass Spectrometry. Methods Mol Med. 2003;89:465-478. [PubMed]

Disease research

1. Lorenz P, Ruschpler P, Koczan D, Stiehl P, Thiesen HJ. From transcriptome to proteome: Differentially expressed proteins identified in synovial tissue of patients suffering from rheumatoid arthritis and osteoarthritis by an initial screen with a panel of 791 antibodies. Proteomics. 2003 Jun;3(6):991-1002. [PubMed]
2. Celis JE, Gromov P, Gromova I, Moreira JM, Cabezon T, Ambartsumian N, Grigorian M, Lukanidin E, Thor Straten P, Guldberg P, Bartkova J, Bartek J, Lukas J, Lukas C, Lykkesfeldt A, Jaattela M, Roepstorff P, Bolund L, Orntoft T, Brunner N, Overgaard J, Sandelin K, Blichert-Toft M, Mouridsen H, Rank FE. Integrating proteomic and functional genomic technologies in discovery-driven translational breast cancer research. Mol Cell Proteomics. 2003 Jun 27 [Epub ahead of print] [PubMed]
3. Klose J. Mouse models for neurodegenerative diseases and a theory of proteomics. J Neurochem. 2003 Jun;85 Suppl 2:8. [PubMed]
4. Sagi D. Proteomics in neurodegenerative diseases. J Neurochem. 2003 Jun;85 Suppl 2:19. [PubMed]
5. Baak JP, Path FR, Hermsen MA, Meijer G, Schmidt J, Janssen EA. Genomics and proteomics in cancer. Eur J Cancer. 2003 Jun;39(9):1199-215. [PubMed]
6. Bandara LR, Kelly MD, Lock EA, Kennedy S. A potential biomarker of kidney damage identified by proteomics: preliminary findings. Biomarkers. 2003 May-Jun;8(3-4):272-86. [PubMed]   
7. Denslow N, Michel ME, Temple MD, Hsu CY, Saatman K, Hayes RL. Application of proteomics technology to the field of neurotrauma. J Neurotrauma. 2003 May;20(5):401-7. [PubMed]
8. Hondermarck H. Breast cancer: when proteomics challenges biological complexity. Mol Cell Proteomics. 2003 May 29 [Epub ahead of print] [PubMed]
9. He QY, Lau GK, Zhou Y, Yuen ST, Lin MC, Kung HF, Chiu JF. Serum biomarkers of hepatitis B virus infected liver inflammation: A proteomic study. Proteomics. 2003 May;3(5):666-74. [PubMed]
10. Zhan X, Desiderio DM. A reference map of a human pituitary adenoma proteome. Proteomics. 2003 May;3(5):699-713. [PubMed]
11. Schoneich C. Proteomics in gerontological research. Exp Gerontol. 2003 May;38(5):473-81. [PubMed]
12. Nicolls MR, D'Antonio JM, Hutton JC, Gill RG, Czwornog JL, Duncan MW. Proteomics as a tool for discovery: proteins implicated in Alzheimer's disease are highly expressed in normal pancreatic islets. J Proteome Res. 2003 Mar-Apr;2(2):199-205. [PubMed]
13. Oehr P. Proteomics as a tool for detection of nuclear matrix proteins and new biomarkers for screening of early tumors stage. Anticancer Res. 2003 Mar-Apr;23(2A):805-12. [PubMed]
14. You SA, Archacki SR, Angheloiu G, Moravec CS, Rao S, Kinter M, Topol EJ, Wang Q. Proteomic approach to coronary atherosclerosis shows ferritin light chain as a significant marker: evidence consistent with iron hypothesis in atherosclerosis. Physiol Genomics. 2003 Mar 18;13(1):25-30. [PubMed]
15. Sellers TA, Yates JR. Review of proteomics with applications to genetic epidemiology. Genet Epidemiol. 2003 Feb;24(2):83-98. [PubMed]
16. Celis JE, Gromov P. Proteomics in translational cancer research: Toward an integrated approach. Cancer Cell. 2003 Jan;3(1):9-15. [PubMed]
17. Ahram M, Emmert-Buck MR. Approaches to proteomic analysis of human tumors. Methods Mol Biol. 2003;222:375-84. [PubMed]
18. Naaby-Hansen S, Nagano K, Gaffney P, Masters JR, Cramer R. Proteomics in the analysis of prostate cancer. Methods Mol Med. 2003;81:277-97. [PubMed]
19. Steinert R, Von Hoegen P, Fels LM, Gunther K, Lippert H, Reymond MA. Proteomic prediction of disease outcome in cancer : clinical framework and current status. Am J Pharmacogenomics. 2003;3(2):107-15. [PubMed]

Clinical application

1. Celis JE. Clinical proteomics: an emerging discipline in biomedical research. Mol Cell Proteomics. 2003 Jun;2(6):367. [PubMed]
2. Wulfkuhle JD, Liotta LA, Petricoin EF. Early detection: Proteomic applications for the early detection of cancer. Nat Rev Cancer. 2003 Apr;3(4):267-75. [PubMed]
3. Yeatman TJ. The future of cancer management: translating the genome, transcriptome, and proteome. Ann Surg Oncol. 2003 Jan-Feb;10(1):7-14. [PubMed]
4. Zheng PP, Kros JM, Sillevis-Smitt PA, Theo M Luider Fn FM. Proteomics in primary brain tumors. Front Biosci. 2003 Jan 1;8:D451-63. [PubMed]
5. Steinert R, Von Hoegen P, Fels LM, Gunther K, Lippert H, Reymond MA. Proteomic prediction of disease outcome in cancer : clinical framework and current status. Am J Pharmacogenomics. 2003;3(2):107-15. [PubMed]
6. Wulfkuhle JD, Paweletz CP, Steeg PS, Petricoin EF 3rd, Liotta L. Proteomic approaches to the diagnosis, treatment, and monitoring of cancer. Adv Exp Med Biol. 2003;532:59-68. [PubMed]

Pharmacogenomics

1. Poirier F, Joubert-Caron R, Labas V, Caron M. Proteomic analysis of a lymphoma-derived cell line (DG75) following treatment with a demethylating drug: Modification of membrane-associated proteins. Proteomics. 2003 Jun;3(6):1028-36. [PubMed]
2. Verrills NM, Kavallaris M. Drug resistance mechanisms in cancer cells: a proteomics perspective. Curr Opin Mol Ther. 2003 Jun;5(3):258-65. [PubMed]
3. Armandola EA. Proteomics and new therapeutic strategies. MedGenMed. 2003 May 22;5(2):21. [PubMed]
4. Oda Y, Owa T, Sato T, Boucher B, Daniels S, Yamanaka H, Shinohara Y, Yokoi A, Kuromitsu J, Nagasu T. Quantitative Chemical Proteomics for Identifying Candidate Drug Targets. Anal Chem. 2003 May 1;75(9):2159-2165. [PubMed]
5. Petri WA. Can a proteomics strategy be used to identify the anti-malarial activity of chloroquine? Trends Pharmacol Sci. 2003 May;24(5):210-2. [PubMed]
6. Haystead TA. Response to Petri: Can a proteomics strategy be used to identify the anti-malarial activity of chloroquine? Trends Pharmacol Sci. 2003 May;24(5):212-3. [PubMed]
7. Archakov AI, Govorun VM, Dubanov AV, Ivanov YD, Veselovsky AV, Lewi P, Janssen P. Protein-protein interactions as a target for drugs in proteomics. Proteomics. 2003 Apr;3(4):380-91. [PubMed]
8. Valle RP, Jendoubi M. Antibody-based technologies for target discovery. Curr Opin Drug Discov Devel. 2003 Mar;6(2):197-203. [PubMed]
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10. Witzmann FA, Grant RA. Pharmacoproteomics in drug development. Pharmacogenomics J. 2003;3(2):69-76. [PubMed]
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Structural genomics

1. Structural biology: The crystal's in the mail... Nature. 2003 Jun 19; [PubMed]
2. Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M. SPINE 2: a system for collaborative structural proteomics within a federated database framework. Nucleic Acids Res. 2003 Jun 1;31(11):2833-8. [PubMed]
3. Kimber MS, Vallee F, Houston S, Necakov A, Skarina T, Evdokimova E, Beasley S, Christendat D, Savchenko A, Arrowsmith CH, Vedadi M, Gerstein M, Edwards AM. Data mining crystallization databases: Knowledge-based approaches to optimize protein crystal screens. Proteins. 2003 Jun 1;51(4):562-8. [PubMed]
4. Lee D. et al., A structural perspective on genome evolution. Curr Opin Struct Biol. 2003 Jun; [PubMed]
5. Rodrigues A, Hubbard RE. Making decisions for structural genomics. Brief Bioinform. 2003 Jun;4(2):150-67. [PubMed]
6. Zeri AC, Mesleh MF, Nevzorov AA, Opella SJ. Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy. Proc Natl Acad Sci U S A. 2003 May 27;100(11):6458-63. [PubMed][pdf]
7. Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM. Integrating structure, bioinformatics and enzymology to discover function: BioH, a new carboxylesterase from E. coli. J Biol Chem. 2003 May 5 [epub ahead of print] [PubMed]
8. Lefkovits I. Functional and structural proteomics: a critical appraisal. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):1-10. [PubMed]
9. van der Woerd M, Ferree D, Pusey M. The promise of macromolecular crystallization in microfluidic chips. J Struct Biol. 2003 Apr;142(1):180-7. [PubMed]
10. Wingren C, Edmundson AB, Borrebaeck CA. Designing proteins to crystallize through beta-strand pairing. Protein Eng. 2003 Apr;16(4):255-64. [PubMed]
11. Gerstein M, Edwards A, Arrowsmith CH, Montelione GT. Structural genomics: current progress. Science. 2003 Mar 14;299(5613):1663. [PubMed]
12. Torres J, Stevens TJ, Samso M. Membrane proteins: the 'Wild West' of structural biology. Trends Biochem Sci. 2003 Mar;28(3):137-44. [PubMed]
13. Yee A, Pardee K, Christendat D, Savchenko A, Edwards AM, Arrowsmith CH. Structural proteomics: toward high-throughput structural biology as a tool in functional genomics. Acc Chem Res. 2003 Mar;36(3):183-9. [PubMed]
14. Adams MW, Dailey HA, DeLucas LJ, Luo M, Prestegard JH, Rose JP, Wang BC. The southeast collaboratory for structural genomics: a high-throughput gene to structure factory. Acc Chem Res. 2003 Mar;36(3):191-8. [PubMed]
15. Banci L, Rosato A. Structural genomics of proteins involved in copper homeostasis. Acc Chem Res. 2003 Mar;36(3):215-21. [PubMed]
16. Savchenko A, Yee A, Khachatryan A, Skarina T, Evdokimova E, Pavlova M, Semesi A, Northey J, Beasley S, Lan N, Das R, Gerstein M, Arrowmith CH, Edwards AM. Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches. Proteins. 2003 Feb 15;50(3):392-9. [PubMed]
17. Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L, Lichtarge O. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol. 2003 Feb 7;326(1):255-61. [PubMed]
18. Taylor PW, Stapleton PD. Structural pharmacogenomics: the answer to antimicrobial drug resistance? Drug Discov Today. 2003 Feb 1;8(3):110-1. [PubMed]
19. Zhang C, Kim SH. Overview of strucutral genomics: from structure to function. Curr Opin Chem Biol. 2003 Feb; 7:28-32. [PubMed]
20. Yang JK, Park MS, Waldo GS, Suh SW. Directed evolution approach to a structural genomics project: Rv2002 from Mycobacteriumtuberculosis. Proc Natl Acad Sci U S A 2003 Jan 21;100(2):455-60 [PubMed][pdf]
21. Eswaramoorthy S, Gerchman S, Graziano V, Kycia H, Studier FW, Swaminathan S. Structure of a yeast hypothetical protein selected by a structural genomics approach. Acta Crystallogr D Biol Crystallogr. 2003 Jan 1;59(Pt 1):127-135. [PubMed]
22. Bruschweiler R. Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation. Proteins. 2003 Jan 1;50(1):26-34. [PubMed]
23. Zhang YM, Marrakchi H, White SW, Rock CO. The application of computational methods to explore the diversity and structure of bacterial fatty acid synthase. J Lipid Res. 2003 Jan;44(1):1-10. [PubMed]
24. Marassi F. Utilizing NMR to study the structure of growth-inhibitory proteins. Methods Mol Biol. 2003;223:3-16. [PubMed]
25. Dihazi GH, Sinz A. Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom. 2003;17(17):2005-14. [PubMed]
26. Naylor S, Kumar R. Emerging role of mass spectrometry in structural and functional proteomics. Adv Protein Chem. 2003;65:217-48. [PubMed]

Technical developments

1. Claverol S, Burlet-Schiltz O, Gairin JE, Monsarrat B. Characterization of protein variants and post-translational modifications: ESI-MSn analyses of intact proteins eluted from polyacrylamide gels. Mol Cell Proteomics. 2003 Jun 27 [Epub ahead of print] [PubMed]
2. Freeze H. Mass spectrometry provides sweet inspiration. Nat Biotechnol. 2003 Jun;21(6):627-9. [PubMed]
3. Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol. 2003 Jun;21(6):660-6. [PubMed][web supplement]
4. Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol. 2003 Jun;21(6):667-72. [PubMed][web supplement]
5. Leung D, Hardouin C, Boger DL, Cravatt BF. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat Biotechnol. 2003 Jun;21(6):687-691. [PubMed][web supplement]
6. Bradbury A, Velappan N, Verzillo V, Ovecka M, Chasteen L, Sblattero D, Marzari R, Lou J, Siegel R, Pavlik P. Antibodies in proteomics I: generating antibodies. Trends Biotechnol. 2003 Jun;21(6):275-81. [PubMed]
7. McDonald WH, Yates JR 3rd. Shotgun proteomics: integrating technologies to answer biological questions. Curr Opin Mol Ther. 2003 Jun;5(3):302-9. [PubMed]
8. Pedersen SK, Harry JL, Sebastian L, Baker J, Traini MD, McCarthy JT, Manoharan A, Wilkins MR, Gooley AA, Righetti PG, Packer NH, Williams KL, Herbert BR. Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins. J Proteome Res. 2003 May-Jun;2(3):303-11. [PubMed]
9. Tabuchi I. Next-generation protein-handling method: puromycin analogue technology. Biochem Biophys Res Commun. 2003 May 23;305(1):1-5. [PubMed]
10. Berhane BT, Limbach PA. Functional Microfabricated Sample Targets for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Ribonucleic Acids. Anal Chem. 2003 May 1;75(9):1997-2003. [PubMed]
11. Rabilloud T. Membrane proteins ride shotgun. Nat Biotechnol. 2003 May;21(5):508-10. [PubMed]
12. Wu CC, MacCoss MJ, Howell KE, Yates JR. A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 2003 May;21(5):532-8 [PubMed][web supplement]
13. Serikawa KA, Xu XL, MacKay VL, Law GL, Zong Q, Zhao LP, Bumgarrner R, Morris DR. The transcriptome and its translation during recovery from cell-cycle arrest in Saccharomyces cerevisiae. Mol Cell Proteomics. 2003 Apr 7 [epub ahead of print] [PubMed]
14. Yao X, Afonso C, Fenselau C. Dissection of proteolytic 18O labeling: endoprotease-catalyzed 16O-to-18O exchange of truncated peptide substrates. J Proteome Res. 2003 Mar-Apr;2(2):147-52. [PubMed]
15. Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates JR 3rd. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3107-3112. [PubMed][pdf][web supplement]
16. Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, Aebersold R. The study of macromolecular complexes by quantitative proteomics. Nat Genet 2003 Mar;33(3):349-55 [PubMed]
17. Ansari AZ. Fingers reach for the genome. Nat Biotechnol. 2003 Mar;21(3):242-3. [PubMed]
18. Blancafort P, Magnenat L, Barbas CF. Scanning the human genome with combinatorial transcription factor libraries. Nat Biotechnol. 2003 Mar;21(3):269-74. [PubMed][web supplement]
19. Bae KH, Do Kwon Y, Shin HC, Hwang MS, Ryu EH, Park KS, Yang HY, Lee DK, Lee Y, Park J, Sun Kwon H, Kim HW, Yeh BI, Lee HW, Hyung Sohn S, Yoon J, Seol W, Kim JS. Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat Biotechnol. 2003 Mar;21(3):275-80. [PubMed][web supplement]
20. Bonenfant D, Schmelzle T, Jacinto E, Crespo JL, Mini T, Hall MN, Jenoe P. Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry. Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):880-5. [PubMed]
21. Dreger M. Proteome analysis at the level of subcellular structures. Eur J Biochem. 2003 Feb;270(4):589-99. [PubMed]
22. Taylor SW, Fahy E, Ghosh SS. Global organellar proteomics. Trends Biotechnol. 2003 Feb;21(2):82-8. [PubMed]
23. Xin W, Ma J, Huang DW. Construction of linear functional expression elements with DNA and RNA hybrid primers: a flexible and fast method for proteomics. Biotechnol Lett. 2003 Feb;25(3):273-7. [PubMed]
24. Beardsley RL, Reilly JP. Quantitation using enhanced signal tags: a technique for comparative proteomics. J Proteome Res. 2003 Jan-Feb;2(1):15-21. [PubMed]
25. Roegener J, Lutter P, Reinhardt R, Bluggel M, Meyer HE, Anselmetti D. Ultrasensitive detection of unstained proteins in acrylamide gels by native UV fluorescence. Anal Chem. 2003 Jan 1;75(1):157-9. [PubMed]
26. Loo JA. The tools of proteomics. Adv Protein Chem. 2003;65:25-56. [PubMed]
27. Sebastiano R, Citterio A, Lapadula M, Righetti PG. A new deuterated alkylating agent for quantitative proteomics. Rapid Commun Mass Spectrom. 2003;17(21):2380-6. [PubMed]
28. Hayes F. Transposon-based strategies for microbial functional genomics and proteomics. Annu Rev Genet. 2003;37:3-29. [PubMed]

Protein expression techniques

1. Busso D, Kim R, Kim SH. Expression of soluble recombinant proteins in a cell-free system using a 96-well format. J Biochem Biophys Methods. 2003 Mar 28;55(3):233-40. [PubMed]
2. Rappsilber J, Ishihama Y, Mann M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem. 2003 Feb 1;75(3):663-70. [PubMed]
3. Yokoyama S. Protein expression systems for structural genomics and proteomics. Curr Opin Chem Biol. 2003 Feb; 7:39-43. [PubMed]
   

2D gel; Protein purification and chromatographic techniques

1. Lecchi P, Gupte AR, Perez RE, Stockert LV, Abramson FP. Size-exclusion chromatography in multidimensional separation schemes for proteome analysis. J Biochem Biophys Methods. 2003 Jun 30;56(1-3):141-52. [PubMed]
2. Lion N, Gellon JO, Jensen H, Girault HH. On-chip protein sample desalting and preparation for direct coupling with electrospray ionization mass spectrometry. J Chromatogr A. 2003 Jun 27;1003(1-2):11-9. [PubMed]
3. Werner WE. Run parameters affecting protein patterns from second dimension electrophoresis gels. Anal Biochem. 2003 Jun 15;317(2):280-3. [PubMed]
4. Lee BS, Gupta S, Morozova I. High-resolution separation of proteins by a three-dimensional sodium dodecyl sulfate polyacrylamide cube gel electrophoresis. Anal Biochem. 2003 Jun 15;317(2):271-5. [PubMed]
5. Kery V, Savage JR, Widjaja K, Kelly Blake B, Conklin DR, Ho YS, Long X, von Rechenberg M, Zarembinski TI, Jay Boniface J. Expression screen by enzyme-linked immunofiltration assay designed for high-throughput purification of affinity-tagged proteins. Anal Biochem. 2003 Jun 15;317(2):255-8. [PubMed]
6. Romijn EP, Krijgsveld J, Heck AJ. Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics. J Chromatogr A. 2003 Jun 6;1000(1-2):589-608. [PubMed]
7. Zhan X, Desiderio DM. Spot volume vs. amount of protein loaded onto a gel: A detailed, statistical comparison of two gel electrophoresis systems. Electrophoresis. 2003 Jun;24(11):1818-33. [PubMed]
8. Ren D, Penner NA, Slentz BE, Mirzaei H, Regnier F. Evaluating immobilized metal affinity chromatography for the selection of histidine-containing peptides in comparative proteomics. J Proteome Res. 2003 May-Jun;2(3):321-9. [PubMed]
9. Kjellstrom S, Jensen ON. In situ liquid-liquid extraction as a sample preparation method for matrix-assisted laser desorption/ionization MS analysis of polypeptide mixtures. Anal Chem. 2003 May 15;75(10):2362-9. [PubMed]
10. Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, Thomas GR, Vandekerckhove J. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 2003 May;21(5):566-9 [PubMed][web supplement]
11. Kline TR, Pang J, Hefta SA, Opiteck GJ, Kiefer SE, Scheffler JE. A high-yield method to extract peptides from rat brain tissue. Anal Biochem. 2003 Apr 15;315(2):183-8. [PubMed]
12. Xiang R, Horvath C, Wilkins JA. Elution-modified displacement chromatography coupled with electrospray ionization-MS: on-line detection of trace peptides at low-femtomole level in peptide digests. Anal Chem. 2003 Apr 15;75(8):1819-27. [PubMed]
13. Wang H, Hanash S. Multi-dimensional liquid phase based separations in proteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):11-8. [PubMed]
14. Van Den Bergh G, Clerens S, Cnops L, Vandesande F, Arckens L. Fluorescent two-dimensional difference gel electrophoresis and mass spectrometry identify age-related protein expression differences for the primary visual cortex of kitten and adult cat. J Neurochem. 2003 Apr;85(1):193-205. [PubMed]
15. Pieper R, Su Q, Gatlin CL, Huang ST, Anderson NL, Steiner S. Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome. Proteomics. 2003 Apr;3(4):422-32. [PubMed]
16. Campbell DA, Szardenings AK. Functional profiling of the proteome with affinity labels. Curr Opin Chem Biol. Apr; 7: 296-303. [PubMed]
17. Thevis M, Ogorzalek Loo RR, Loo JA. In-gel derivatization of proteins for cysteine-specific cleavages and their analysis by mass spectrometry. J Proteome Res. 2003 Mar-Apr;2(2):163-72. [PubMed]
18. Goshe MB, Blonder J, Smith RD. Affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis. J Proteome Res. 2003 Mar-Apr;2(2):153-61. [PubMed]
19. Kimura A, Adachi N, Horikoshi M. Series of vectors to evaluate the position and the order of two different affinity tags for purification of protein complexes. Anal Biochem. 2003 Mar 15;314(2):253-9. [PubMed]
20. Luche S, Santoni V, Rabilloud T. Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics. 2003 Mar;3(3):249-53. [PubMed]
21. Wang YY, Cheng PC, Chan DW. A simple affinity spin tube filter method for removing high-abundant common proteins or enriching low-abundant biomarkers for serum proteomic analysis. Proteomics. 2003 Mar;3(3):243-248. [PubMed]
22. Fountoulakis M, Juranville JF. Enrichment of low-abundance brain proteins by preparative electrophoresis. Anal Biochem. 2003 Feb 15;313(2):267-82. [PubMed]
23. Bauer A, Kuster B. Affinity purification-mass spectrometry. Eur J Biochem. 2003 Feb;270(4):570-8. [PubMed]
24. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I. A novel experimental design for comparative two-dimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics. 2003 Jan;3(1):36-44. [PubMed]
25. Forler D, Kocher T, Rode M, Gentzel M, Izaurralde E, Wilm M. An efficient protein complex purification method for functional proteomics in higher eukaryotes. Nat Biotechnol 2003 Jan;21(1):89-92 [PubMed]
26. Ronai Z, Wang Y, Khandurina J, Budworth P, Sasvari-Szekely M, Wang X, Guttman A. Transcription factor binding study by capillary zone electrophoretic mobility shift assay. Electrophoresis. 2003 Jan;24(1-2):96-100. [PubMed]
27. Michel PE, Reymond F, Arnaud IL, Josserand J, Girault HH, Rossier JS. Protein fractionation in a multicompartment device using Off-Gel trade mark isoelectric focusing. Electrophoresis. 2003 Jan;24(1-2):3-11. [PubMed]
28. Giorgianni F, Desiderio DM, Beranova-Giorgianni S. Proteome analysis using isoelectric focusing in immobilized pH gradient gels followed by mass spectrometry. Electrophoresis. 2003 Jan;24(1-2):253-9. [PubMed]
29. Katayama H, Satoh K, Takeuchi M, Deguchi-Tawarada M, Oda Y, Nagasu T. Optimization of in-gel protein digestion system in combination with thin-gel separation and negative staining in 96-well plate format. Rapid Commun Mass Spectrom. 2003;17(10):1071-8. [PubMed]
30. Ihling C, Berger K, Hofliger MM, Fuhrer D, Beck-Sickinger AG, Sinz A. Nano-high-performance liquid chromatography in combination with nano-electrospray ionization Fourier transform ion-cyclotron resonance mass spectrometry for proteome analysis. Rapid Commun Mass Spectrom. 2003;17(12):1240-6. [PubMed]
31. Belov ME, Rakov VS, Nikolaev EN, Goshe MB, Anderson GA, Smith RD. Initial implementation of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control. Rapid Commun Mass Spectrom. 2003;17(7):627-36. [PubMed]
32. Issaq HJ. Application of separation technologies to proteomics research. Adv Protein Chem. 2003;65:249-69. [PubMed]
33. Smith RD, Anderson GA, Lipton MS, Masselon C, Pasa-Tolic L, Udseth H, Belov M, Shen Y, Veenstra TD. High-performance separations and mass spectrometric methods for high-throughput proteomics using accurate mass tags. Adv Protein Chem. 2003;65:85-131. [PubMed]

Mass spectrometry

1. Suckau D, Resemann A, Schuerenberg M, Hufnagel P, Franzen J, Holle A. A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal Bioanal Chem. 2003 Jun 27 [Epub ahead of print] [PubMed]
2. Romijn EP, Krijgsveld J, Heck AJ. Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics. J Chromatogr A. 2003 Jun 6;1000(1-2):589-608. [PubMed]
3. Le Blanc JC, Hager JW, Ilisiu AM, Hunter C, Zhong F, Chu I. Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications. Proteomics. 2003 Jun;3(6):859-69. [PubMed]
4. Bergquist J. FTICR mass spectrometry in proteomics. Curr Opin Mol Ther. 2003 Jun;5(3):310-4. [PubMed]
5. Miller CA, Yi D, Perkins PD. An atmospheric pressure matrix-assisted laser desorption/ionization ion trap with enhanced sensitivity. Rapid Commun Mass Spectrom. 2003 Apr 30;17(8):860-868. [PubMed]
6. Lin D, Tabb DL, Yates JR. Large-scale protein identification using mass spectrometry. Biochim Biophys Acta. 2003 Mar 21;1646(1-2):1-10. [PubMed]
7. Yague J, Paradela A, Ramos M, Ogueta S, Marina A, Barahona F, Lopez de Castro JA, Vazquez J. Peptide rearrangement during quadrupole ion trap fragmentation: added complexity to MS/MS spectra. Anal Chem. 2003 Mar 15;75(6):1524-35. [PubMed]
8. Griffin TJ, Lock CM, Li XJ, Patel A, Chervetsova I, Lee H, Wright ME, Ranish JA, Chen SS, Aebersold R. Abundance ratio-dependent proteomic analysis by mass spectrometry. Anal Chem. 2003 Feb 15;75(4):867-74. [PubMed]
9. McLean JA, Russell WK, Russell DH. A high repetition rate (1 kHz) microcrystal laser for high throughput atmospheric pressure MALDI-quadrupole-time-of-flight mass spectrometry. Anal Chem. 2003 Feb 1;75(3):648-54. [PubMed]
10. Bauer A, Kuster B. Affinity purification-mass spectrometry. Eur J Biochem. 2003 Feb;270(4):570-8. [PubMed]
11. Dreger M. Emerging strategies in mass-spectrometry based proteomics. Eur J Biochem. 2003 Feb;270(4):569. [PubMed]
12. Sechi S, Oda Y.  Quantitative proteomics using mass spectrometry. Curr Opin Chem Biol. 2003 Feb; 7:70-77. [PubMed]
13. Tao WA, Aebersold R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry.Curr Opin Biotechnol. 2003 Feb;14(1):110-8. [PubMed]
14. Goshe MB, Smith RD. Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol. 2003 Feb;14(1):101-9. [PubMed]
15. Ong SE, Foster LJ, Mann M. Mass spectrometric-based approaches in quantitative proteomics. Methods. 2003 Feb;29(2):124-30. [PubMed]
16. Gu S, Pan S, Bradbury EM, Chen X. Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging. J Am Soc Mass Spectrom. 2003 Jan;14(1):1-7. [PubMed]
17. Giorgianni F, Desiderio DM, Beranova-Giorgianni S. Proteome analysis using isoelectric focusing in immobilized pH gradient gels followed by mass spectrometry. Electrophoresis. 2003 Jan;24(1-2):253-9. [PubMed]
18. Belov ME, Rakov VS, Nikolaev EN, Goshe MB, Anderson GA, Smith RD. Initial implementation of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control. Rapid Commun Mass Spectrom. 2003;17(7):627-36. [PubMed]

Protein-protein interaction study

1. Scheibner KA, Zhang Z, Cole PA. Merging fluorescence resonance energy transfer and expressed protein ligation to analyze protein-protein interactions. Anal Biochem. 2003 Jun 15;317(2):226-32. [PubMed]
2. Zhu MM, Rempel DL, Du Z, Gross ML. Quantification of Protein-Ligand Interactions by Mass Spectrometry, Titration, and H/D Exchange: PLIMSTEX. J Am Chem Soc. 2003 May 7;125(18):5252-3. [PubMed]
3. Hu CD, Kerppola TK. Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nat Biotechnol 2003 May;21(5):539-45 [PubMed][web supplement]
4. Gururaja TL, Li W, Payan DG, Anderson DC. Utility of peptide-protein affinity complexes in proteomics: identification of interaction partners of a tumor suppressor peptide. J Pept Res. 2003 Apr;61(4):163-76. [PubMed]
5. Lopez F, Pichereaux C, Burlet-Schiltz O, Pradayrol L, Monsarrat B, Esteve JP. Improved sensitivity of biomolecular interaction analysis mass spectrometry for the identification of interacting molecules. Proteomics. 2003 Apr;3(4):402-12. [PubMed]
6. Drewes G, Bouwmeester T. Global approaches to protein-protein interactions. Curr Opin Cell Biol. 2003 Apr;15(2):199-205. [PubMed]
7. Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol. 2003 Mar;21(3):315-8. [PubMed][web supplement]
8. Arkin MR, Randal M, DeLano WL, Hyde J, Luong TN, Oslob JD, Raphael DR, Taylor L, Wang J, McDowell RS, Wells JA, Braisted AC. Binding of small molecules to an adaptive protein-protein interface. Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1603-8. [PubMed][pdf][web supplement]
9. Sidhu SS, Bader GD, Boone C.  Functional genomics of intracellular peptide recognition domains with combinatorial biology methods. Curr Opin Chem Biol. 2003 Feb; 7: 97-102. [PubMed]
10. Turk BE, Cantley LC.  Peptide libraries: at the crossroads of proteomics and bioinformatics. Curr Opin Chem Biol. 2003 Feb; 7:84-90. [PubMed]

Protein function study

1. Kupcho K, Somberg R, Bulleit B, Goueli SA. A homogeneous, nonradioactive high-throughput fluorogenic protein kinase assay. Anal Biochem. 2003 Jun 15;317(2):210-7. [PubMed]
2. Havlis J, Thomas H, Sebela M, Shevchenko A. Fast-response proteomics by accelerated in-gel digestion of proteins. Anal Chem. 2003 Mar 15;75(6):1300-6. [PubMed]
3. Kozarich JW. Activity-based proteomics: enzyme chemistry redux. Curr Opin Chem Biol. 2003 Feb;7(1):78-83. [PubMed]

Post-translational modification study

1. Claverol S, Burlet-Schiltz O, Gairin JE, Monsarrat B. Characterization of protein variants and post-translational modifications: ESI-MSn analyses of intact proteins eluted from polyacrylamide gels. Mol Cell Proteomics. 2003 Jun 27 [Epub ahead of print] [PubMed]
2. Mann M, Jensen ON. Proteomic analysis of post-translational modifications. Nat Biotechnol. 2003 Mar;21(3):255-61. [PubMed]
3. Kalume DE, Molina H, Pandey A. Tackling the phosphoproteome: tools and strategies. Curr Opin Chem Biol. 2003 Feb; 7:64-69. [PubMed]
4. Pelech S, Sutter C, Zhang H. Kinetworks protein kinase multiblot analysis. Methods Mol Biol. 2003;218:99-111. [PubMed]

Data analysis

1. Sorace JM, Zhan M. A Data Review and Re-assessment of Ovarian Cancer Serum Proteomic Profiling. BMC Bioinformatics. 2003 Jun 9 [Epub ahead of print] [PubMed][pdf]
2. Chen Y, Xu D. Computational analyses of high-throughput protein-protein interaction data. Curr Protein Pept Sci. 2003 Jun;4(3):159-81. [PubMed]
3. Lu L, Arakaki AK, Lu H, Skolnick J. Multimeric Threading-Based Prediction of Protein-Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome. Genome Res. 2003 Jun;13(6):1146-54. [PubMed][pdf]
4. Salwinski L, Eisenberg D. Computational methods of analysis of protein–protein interactions. Curr Opin Struct Biol. 2003 Jun;13(3):377-82.  [PubMed]
5. Hernandez P, Gras R, Frey J, Appel RD. Popitam: Towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics. 2003 Jun;3(6):870-8. [PubMed]
6. Kinoshita K, Nakamura H. Protein informatics towards function identification. Curr Opin Struct Biol. 2003 Jun;13(3):396-400. [PubMed]
7. Cai YD, Chou KC. Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition. Biochem Biophys Res Commun. 2003 May 30;305(2):407-11. [PubMed]
8. Haley-Vicente D, Edwards DJ. Proteomic informatics: in silico methods lead to data management challenges. Curr Opin Drug Discov Devel. 2003 May;6(3):322-32. [PubMed]
9. Saito R, Suzuki H, Hayashizaki Y. Construction of reliable protein-protein interaction networks with a new interaction generality measure. Bioinformatics. 2003 Apr 12;19(6):756-63. [PubMed]
10. Anderson DC, Li W, Payan DG, Noble WS. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J Proteome Res. 2003 Mar-Apr;2(2):137-46. [PubMed]
11. Malmstrom L, Malmstrom J, Marko-Varga G, Westergren-Thorsson G. Proteomic 2DE database for spot selection, automated annotation, and data analysis. J Proteome Res. 2002 Mar-Apr;1(2):135-8. [PubMed]
12. Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol. 2003 Mar;21(3):247-54. [PubMed]
13. Patterson SD. Data analysis-the Achilles heel of proteomics. Nat Biotechnol. 2003 Mar;21(3):221-2. [PubMed]
14. Strittmatter EF, Rodriguez N, Smith RD. High mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry. Anal Chem. 2003 Feb 1;75(3):460-8. [PubMed]
15. Lan N, Montelione GT, Gerstein M. Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level. Curr Opin Chem Biol. 2003 Feb; 7:44-54. [PubMed]
16. Marengo E, Robotti E, Gianotti V, Righetti PG. A new approach to the statistical treatment of 2D-maps in proteomics using fuzzy logic. Ann Chim. 2003 Jan-Feb;93(1-2):105-16. [PubMed]
17. Bock JR, Gough DA. Whole-proteome interaction mining. Bioinformatics. 2003 Jan;19(1):125-134. [PubMed]
18. Ju BH, Park B, Park JH, Han K. Visualization and analysis of protein interactions. Bioinformatics. 2003 Jan;19(2):317-8. [PubMed]
19. Pietrogrande MC, Marchetti N, Dondi F, Righetti PG. Spot overlapping in two-dimensional polyacrylamide gel electrophoresis maps: Relevance to proteomics. Electrophoresis. 2003 Jan;24(1-2):217-24. [PubMed]
20. Giometti CS. Proteomics and bioinformatics. Adv Protein Chem. 2003;65:353-69. [PubMed]

Software

1. Wong JW, Downard KM. COMPLX: a computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra. J Mass Spectrom. 2003 May;38(5):573-81. [PubMed]
2. Malmstrom L, Malmstrom J, Marko-Varga G, Westergren-Thorsson G. Proteomic 2DE database for spot selection, automated annotation, and data analysis. J Proteome Res. 2002 Mar-Apr;1(2):135-8. [PubMed]
3. Bennett SP, Nevill-Manning CG, Brutlag DL. 3MOTIF: visualizing conserved protein sequence motifs in the protein structure database. Bioinformatics. 2003 Mar;19(4):541-2.  [PubMed]
   

Database

1. Suzuki H, Saito R, Kanamori M, Kai C, Schonbach C, Nagashima T, Hosaka J, Hayashizaki Y. The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer. Genome Res. 2003 Jun;13(6B):1534-41. [PubMed][pdf]
2. Malmstrom L, Malmstrom J, Marko-Varga G, Westergren-Thorsson G. Proteomic 2DE database for spot selection, automated annotation, and data analysis. J Proteome Res. 2002 Mar-Apr;1(2):135-8. [PubMed]
3. Vierstraete E, Cerstiaens A, Baggerman G, Van den Bergh G, De Loof A, Schoofs L. Proteomics in Drosophila melanogaster: first 2D database of larval hemolymph proteins. Biochem Biophys Res Commun. 2003 May 16;304(4):831-8. [PubMed]
   
4. Lan N, Montelione GT, Gerstein M. Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level. Curr Opin Chem Biol. 2003 Feb; 7:44-54. [PubMed]
5. Medjahed D, Smythers GW, Powell DA, Stephens RM, Lemkin PF, Munroe DJ. VIRTUAL2D: A web-accessible predictive database for proteomics analysis. Proteomics. 2003 Feb;3(2):129-38. [PubMed]
6. Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 2003 Jan 1;31(1):414-7. [PubMed]
7. Carter P, Liu J, Rost B. PEP: Predictions for Entire Proteomes. Nucleic Acids Res. 2003 Jan 1;31(1):410-3. [PubMed]