Services offered:

• Experimental design consultation.
• Sample processing at bench, e.g. in-gel digests; isotopic labeling, e.g. Isotope- Coded Affinity Tags (ICAT™), and Amine-Modifying Labeling Reagents for Relative and Absolute Quantitation (iTRAQ™).
• Sample processing off-line, e.g. cation exchange High-Performance Liquid Chromatography (HPLC).
• Sample processing in-line, e.g. liquid chromatography/tandem mass spectrometry (LC-MS/MS)
• Data analysis through ISB proteomics data analysis pipeline

Equipment and procedures:

Autosamplers:

Dionex FAMOS micro-autosamplers
Agilent 1100

HPLC pumps:

Agilent binary and quaternary microflow HPLC pumps
Agilent quaternary nanoflow HPLC pump

Mass Spectrometers:

Thermo Finnigan LCQ-DECA 3D ion-trap MS
Thermo Finnigan LTQ linear ion-trap MS
Applied Biosystems/Sciex Qstar Pulsar I Q-TOF MS
Waters/Micromass Q-TOF Ultima API MS

• Sample preparation and fractionation for LC-MS/MS including:
  1. a. sample (protein) precipitation, resolubilization, and digestion;
  2. b. sample cleanup (e.g. by off-line reverse-phase method);
  3. c. isotopic labeling by ICAT™ or iTRAQ™ for relative quantitation of proteins in complex samples;
  4. d. off-line strong cation exchange fractionation.
• High-throughput LC-MS/MS
• Data analysis via ISB proteomics data analysis pipeline: Sequest > Peptide Prophet > Protein Prophet > SBEAMS (Systems Biology Experiment Analysis Management System).

Example(s) of projects that use the services of the facility:

• Investigation of drosophila immune response to various pathogenic infections using ICAT™ technique.
• Identification of mammalian proteins that interact with viral epitopes using Tandem-Affinity Purification Tag (TAP-tag) technique.
• Comparison of proteins in mouse bronchoalveolar lavage fluid unique to healthy versus disease state using ICAT™ technique.
• Analysis of protein complement and abundance in halobacterial cells subjected to controlled perturbations in oxygen concentration via iTRAQ™ technique.

Molloy MP, Donohoe S, Brzezinski EE, Kilby GW, Stevenson TI, Baker JD, Goodlett DR, Gage DA. Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling. Proteomics. 2005 Apr;5(5):1204-8.

Hardwidge PR, Rodriguez-Escudero I, Goode D, Donohoe S, Eng J, Goodlett DR, Aebersold R, Finlay BB. Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J Biol Chem. 2004 May 7;279(19):20127-36. Epub 2004 Feb 26.

Zhang J, Goodlett DR, Quinn JF, Peskind E, Kaye JA, Zhou Y, Pan C, Yi E, Eng J, Wang Q, Aebersold RH, Montine TJ. Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. J Alzheimers Dis. 2005 Apr;7(2):125-33. PMID: 15851850 [PubMed - in process]

Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova I, Lange PH, Goodlett DR, Zhou D, Vasicek TJ, Hood L. Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res. 2005 Apr 15;65(8):3081-91. PMID: 15833837 [PubMed - in process]

Yi EC, Li XJ, Cooke K, Lee H, Raught B, Page A, Aneliunas V, Hieter P, Goodlett DR, Aebersold R. Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics. 2005 Feb;5(2):380-7. PMID: 15648049 [PubMed - in process]

Zhang J, Goodlett DR, Peskind ER, Quinn JF, Zhou Y, Wang Q, Pan C, Yi E, Eng J, Aebersold RH, Montine TJ. Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol Aging. 2005 Feb;26(2):207-27. PMID: 15582749 [PubMed - indexed for MEDLINE]

Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. Lipid raft proteins and their identification in T lymphocytes. Subcell Biochem. 2004;37:121-52. Review. PMID: 15376619 [PubMed - indexed for MEDLINE]

Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG. System-based proteomic analysis of the interferon response in human liver cells.Genome Biol. 2004;5(8):R54. Epub 2004 Jul 22. PMID: 15287976 [PubMed - indexed for MEDLINE]

Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE. Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics. 2004 Oct;3(10):960-9. Epub 2004 Jul 6. PMID: 15238602 [PubMed - indexed for MEDLINE]

Lee H, Yi EC, Wen B, Reily TP, Pohl L, Nelson S, Aebersold R, Goodlett DR. Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Apr 15;803(1):101-10. PMID: 15026003 [PubMed - indexed for MEDLINE]

Yi EC, Lee H, Aebersold R, Goodlett DR. A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Commun Mass Spectrom. 2003;17(18):2093-8. PMID: 12955739 [PubMed - indexed for MEDLINE]

10: Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV. Proteomic Analysis of an Extreme Halophilic Archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics. 2003 Aug;2(8):506-24. Epub 2003 Jul 18. PMID: 12872007 [PubMed - in process]

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. PMID: 12867470 [PubMed - indexed for MEDLINE]

Guina T, Wu M, Miller SI, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, Ernst RK, Lee KA. Proteomic analysis of Pseudomonas aeruginosa grown under magnesium limitation. J Am Soc Mass Spectrom. 2003 Jul;14(7):742-51. PMID: 12837596 [PubMed - indexed for MEDLINE]

Shiio Y, Eisenman RN, Yi EC, Donohoe S, Goodlett DR, Aebersold R. Quantitative proteomic analysis of chromatin-associated factors. J Am Soc Mass Spectrom. 2003 Jul;14(7):696-703. PMID: 12837591 [PubMed - indexed for MEDLINE]

Purvine S, Eppel JT, Yi EC, Goodlett DR. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics. 2003 Jun;3(6):847-50. PMID: 12833507 [PubMed - indexed for MEDLINE]

Von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (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. 2003 Jul;2(7):428-42. Epub 2003 Jun 25. PMID: 12832459 [PubMed - in process]

Von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry: I. Statistically Annotated Datasets for Peptide Sequences and Proteins Identified via the Application of ICAT and Tandem Mass Spectrometry to Proteins Copurifying with T Cell Lipid Rafts. Mol Cell Proteomics. 2003 Jul;2(7):426-7. Epub 2003 Jun 25. PMID: 12832456 [PubMed - in process]

Utleg AG, Yi EC, Xie T, Shannon P, White JT, Goodlett DR, Hood L, Lin B. Proteomic analysis of human prostasomes. Prostate. 2003 Jul 1;56(2):150-61. PMID: 12746840 [PubMed - indexed for MEDLINE]

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			Contact information: Dan Martin Phone: 206-732-1365