Seattle Proteome Center (SPC)
NHLBI Proteomics Center at the Institute for Systems Biology

PUBLICATIONS

SPC-related Publications:

A list of publications which have been funded wholly or in part with Federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract No. N01-HV-28179 will be compiled here.

• Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, and Aebersold R. (2003) "The study of macromolecular complexes by quantitative proteomics." Nature Genetics 33(3):349-355.

• Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, Aebersold E. "The study of macromolecular complexes by quantitative proteomics." (2003) Nature Genetics 33(3):349-355

• Mann M and Aebersold R. "Mass spectrometry-based proteomics." (2003) Nature 422(6928):198-207

• Shiio Y, Yi EC, Donohoe S, Goodlett DR, Aebersold R, and Eisenman RN. (2003) "Quantitative proteomic analysis of chromatin-associated factors." J Am Soc Mass Spec 14:696-703.

• Keller A, Nesvizhskii A, Kolker E, and Aebersold R. (2002) "Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search." Anal Chem74:5383-5392.

• Nesvizhskii AI, Keller A, Kolker E, Aebersold R. (2003) "A statistical model for identifying proteins by tandem mass spectrometry." Anal Chem 75:4646-58

• von Haller PD, Yi EC, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, and Watts JD. (2003) "The application of new software tools to quantitative protein profiling via ICAT and tandem mass spectrometry: I. Statistically annotated data sets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins co-purifying with T cell lipid rafts." Mol Cell Proteomics 2(7):426-7.

• von Haller PD, Yi EC, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, and Watts JD. (2003) "The application of new software tools to quantitative protein profiling via ICAT and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis and the application of statistical tools for data analysis and interpretation." Mol Cell Proteomics 2(7):428-42.

• Guina T, Wu M, Miller SI, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, ERnst RK, Lee KA. (2003) "Proteomic analysis of Pseudomonas aeruginosa grown under magnesium limitation." J Am Soc Mass Spec 14:742-751.

• Tao WA and Aebersold R. (2003) "Advances in quantitative proteomics via stable isostope tagging and mass spectrometry." Curr Opin Biotechnol 14:110-118.

• Li X-J, Zhang H, Ranish JR, and Aebersold R. (2003) "Automated statistical analysis of protein abundance ratios from data generated by stable isotope dilution and tandem mass spectrometry." Anal Chem 75:6648-6657.

• Zhang H, Yi EC, Li X-j, Mallick P, Spratt KSK, Masselon CD, Camp DG, Smith RD, Kemp CJ, Aebersold R. (2004) "High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry." Mol. Cell Proteomics 4(2):144-155.

• Flory MR, Carson AR, Muller EG, Aebersold R. (2004) "An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome." Mol Cell 16:1-20.

• Tian Q, Freethman M, Tao WA, He X, Aebersold R, Hood L. (2004) "Proteomic analysis identifies 14-3-3? interacts and stabilizes beta-catenin and facilitates its activation by Akt." Proc. Natl. Acad. Sci. USA 101(43):15370-75.

• Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Dohonoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LW, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R. (2004) "Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry." Genome Biology 6:R9

• Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti R, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK Jr, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. (2004) ""A Common Open Representation of Mass Spectrometry Data and its Application in a Proteomics Research Environment."" Nature Biotechnology 22(11):1459-1466

• Nesvizhskii A, Aebersold R. (2004) "Analysis, statistical validation, and dissemination of large-scale proteomics datasets generated by tandem mass spectrometry." Review in DDT 9(4):173-181.

• Ranish JA, Hahn S, Lu Y, Yi EC, Li XJ, Eng J, Aebersold R. (2004) "Identification of TFB5, a new component of general transcription and DNA repair factor IIH." Nat Genetics 36 (7):707-13.

• Rani PG, Ranish JA, Hahn S. (2004) "RNA polymerase II (Pol II)-TFIIF and Pol II-Mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation." Mol Cell Biol 24(4):1709-20.

• Li X-J, Pedrioli PGA, Eng J, Martin D, Yi EC, Lee H, Aebersold R. (2004) "A tool to visualize and evaluate data obtained by liquid chromatography/electrospray ionization/mass spectrometry." Anal Chem 76:3856-60.

• Brand M, Ranish JA, Kummer NT, Igarashi K, Francastel C, Chi TH, Crabree GR, Aebersold R, and Groudine M. (2004) "Dynamic changes in transcription factors complexes during erythroid differentiation revealed by quantitative proteomics." Nat Structural and Mol Biol 11:73-81.

• Himeda CL, Ranish JA, Angello JC, Maire P, Aebersold R, Hauschka SD. "Quantitative proteomics identification of Six4 as the Trex-binding factor in the muscle creatine kinase enhancer." (2004) Mol Cell Biol 24:2132-43.

• Zhang H, Yan W, Aebersold R. (2004) "Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes."Review in Curr Opinion Chem Biol 8(1):66-75.

• Wollscheid B, Watts J, Aebersold. (2004) "Proteomics/genomics and signaling in lymphocytes." Curr Opin Immunol 16:1-8.

• Schmidt F, Donohoe S, Hagens K, Mattow J, Schaible UE, Kaufmann SHE, Aebersold R, and Jungblat PR. (2004) "Complementary analysis of the mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope coded affinity tag technology." Mol Cell Proteomics 3:24-42.

• Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li X-j, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold RA, Katze MG. (2004) "System-based proteomic analysis of the interferon response in human liver cells." Genome Biology 5:R54.

• Bottari P, Aebersold R, Turecek F, Gelb MH. (2004) "Design and synthesis of visible isotope-coded affinity tags for the absolute quantification of specific proteins in complex mixtures." Bioconjug Chem.15(2):380-8.

• Yan W, Lee H, Deutsch EW, Lazaro CA, Tang W, Chen E, Fausto N, Katze M, Aebersold R. (2004) "A dataset of human liver proteins identified by protein profiling via isotope coded affinity tag (ICAT) and tandem mass spectrometry." Mol Cell Proteomics 10:1039-41.

• Ye M, Lee H, Flory MR, Weber P, Weber G, Eckerskorn C, Aebersold R. (2004) "Free flow electrophoresis-based multidimensional peptide separation for high throughput proteome analysis." (submitted)

• Chen X, Chi Y, Bloecher A, Aebersold R, Clurman BE, Roberts JM. (2004) "N-acetylation and ubiquitin-independent proteasomal degradation of p21Cip1." Mol Cell 16:839-847.

• Gingras AC, Aebersold R, Raught B. "Advances in protein complex analysis using mass spectrometry." (2005) Review in J Physiol 563;1:11-21.

• Pan S, Zhang H, Rush J, Eng J, Zhang N, Patterson D, Comb M, Aebersold R. (2005) "High throughput proteome screening for biomarker detection." Mol Cell Proteomics 4:182-190.

• Marelli M, Smith J, Jung S, Yi E, Nesvizhskii A, Christmas RH, Saleem RA, Tam YY, Faragasanu A, Goodlett D, Aebersold A, Rachubinski RA, Aitchison JD. (2004)"Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin Organization on the peroxisome membrane." J Cell Biology 167(6):1099-1112.

• Chen R, Pan S, Brentnall TA, Aebersold R. (2005) "Proteomic profiling of pancreatic cancer for biomarker discovery." Mol Cell Proteomics 4:523-33.

• Yi EC, Li X-J, Cooke K, Lee H, Raught B, Page A, Aneliunas V, Hieter P, Goodlett DR, Aebersold R. (2005) "Increased quantitative proteome coverage with 13C/12C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme." Proteomics 5:380-87.

• Wright ME, Han DK, Aebersold R. (2005)"Mass spectrometry-based expression profiling of clinical prostate cancer." Mol Cell Proteomics 4:545-554.

• Eng JK, Martin DB, Aebersold R. “Tandem mass spectrometry database searching” In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, 2005.

• Yan W and Chen SS. (2005) "Mass spectrometry-based quantitative proteomic profiling." Briefings in Functional Genomics and Proteomics 4:1-12.

• Tao WA, Wollscheid B, O’Brien R, Eng J, Li X, Bodenmiller B, Watts JD, Hood L, Aebersold R. (2005) "Quantitative phospho-proteomic analysis using a novel dendrimer-based chemistry and mass spectrometry." Nat Methods 2:591-98.

• Kuster B, Schirle M, Mallick P, Aebersold R. (2005) "Scoring proteomes with proteotypic peptide probes." Nat Rev (epub ahead of press).

• Nezvizhskii AI and Aebersold R. (2005) "Interpretation of shotgun proteomics data: the protein inference problem." Molecular and Cellular Proteomics (epub ahead of press).

Suggested Reading:

• Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. "Quantitative analysis of complex protein mixtures using isotope-coded affinity tags." (1999) Nature Biotech 17:994-9.

• Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. "Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology." (2000) Proc Natl Acad Sci USA. 97:9390-5.

• Aebersold R, Goodlett DR. "Mass spectrometry in proteomics." (2001) Chem Rev 101:269-95.

• Aebersold R, Cravatt BF. "Proteomics - advances, applications and the challenges that remain." (2002) Trends Biotechnol 20 (12 Suppl): S1-2.

• Flory MR, Griffin TJ. Aebersold R. "Advances in quantitative proteomics using stable isotope tags." (2002) Trends Biotechnol 20 (12 Suppl): S23-9.

• Patterson SD, Aebersold RH. "Proteomics: the first decade and beyond." (2003)Nature Genetics33(Suppl):311-323.