Evaluation of enrichment techniques for mass spectrometry: Identification of tyrosine phosphoproteins in cancer cells

Journal of Molecular Diagnostics

Volumn 9, Issue 2, 2007, Pages 169-177

  Schumacher, Jonathan A ^a   Crockett, David K ^a   Elenitoba Johnson, Kojo S J ^a,b   Lim, Megan S ^a,b,c  

^a ARUP LABORATORIES   (United States)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANAPLASTIC LYMPHOMA KINASE; NUCLEOPHOSMIN; PHOSPHOPROTEIN; PROTEIN ANTIBODY; PROTEIN TYROSINE KINASE; VANADATE SODIUM; MONOCLONAL ANTIBODY; PHOSPHOTYROSINE; TUMOR PROTEIN; VANADIC ACID;

ARTICLE; CANCER CELL; CELL GROWTH; CELL LYSATE; CONTROLLED STUDY; HUMAN; IMMUNOAFFINITY CHROMATOGRAPHY; IMMUNOPRECIPITATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; TANDEM MASS SPECTROMETRY; AFFINITY CHROMATOGRAPHY; AMINO ACID SEQUENCE; CHEMISTRY; EVALUATION; IMMUNOLOGY; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NEOPLASM; PATHOLOGY; TUMOR CELL LINE;

AMINO ACID SEQUENCE; ANTIBODIES, MONOCLONAL; CELL LINE, TUMOR; CHROMATOGRAPHY, AFFINITY; CHROMATOGRAPHY, LIQUID; HUMANS; IMMUNOPRECIPITATION; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; NEOPLASM PROTEINS; NEOPLASMS; PHOSPHOPROTEINS; PHOSPHOTYROSINE; VANADATES;

EID: 34247862393     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2007.060031     Document Type: Article

References (33)

1. Krause DS, Van Etten RA: Tyrosine kinases as targets for cancer therapy. N Engl J Med 2005, 353:172-187
2. Hunter T: Tyrosine phosphorylation in cell signaling and disease. Keio J Med 2002, 51:61-71
3. Grønborg M, Kristiansen TZ, Stensballe A, Andersen JS, Ohara O, Mann M, Jensen ON, Pandey A: A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol Cell Proteomics 2002, 1:517-527
4. Blume-Jensen P, Hunter T: Oncogenic kinase signalling. Nature 2001, 411:355-365
5. Lugo TG, Pendergast AM, Muller AJ, Witte ON: Tyrosine kinase activity and transformation potency of bcr-abl oncogene products. Science 1990, 247:1079-1082
6. Chabot B, Stephenson DA, Chapman VM, Besmer P, Bernstein A: The proto-oncogene c-kit encoding a transmembrane tyrosine kinase receptor maps to the mouse W locus. Nature 1988, 335:88-89
7. Williams LT: Signal transduction by the platelet-derived growth factor receptor. Science 1989, 243:1564-1570
8. Elmberger PG, Lozano MD, Weisenburger DD, Sanger W, Chan WC: Transcripts of the npm-alk fusion gene in anaplastic large cell lymphoma, Hodgkin's disease, and reactive lymphoid lesions. Blood 1995, 86:3517-3521
9. Imaizumi M, Nishimura M, Takeuchi S, Murase M, Hamaguchi M: Role of tyrosine specific phosphorylation of cellular proteins, especially EGF receptor and p125FAK in human lung cancer cells. Lung Cancer 1997, 17:69-84
10. Ladanyi M, Cavalchire G, Morris SW, Downing J, Filippa DA: Reverse transcriptase polymerase chain reaction for the Ki-1 anaplastic large cell lymphoma-associated t(2;5) translocation in Hodgkin's disease. Am J Pathol 1994, 145:1296-1300
11. Morris SW, Kirstein MN, Valentine MB, Dittmer KG, Shapiro DN, Saltman DL, Look AT: Fusion of a kinase gene, ALK, to a nucleolar protein gene NPM, in non-Hodgkin's lymphoma. Science 1994, 263:1281-1284
12. Pulford K, Lamant L, Morris SW, Butler LH, Wood KM, Stroud D, Delsol G, Mason DY: Detection of anaplastic lymphoma kinase (ALK) and nucleolar protein nucleophosmin (NPM)-ALK proteins in normal and neoplastic cells with the monoclonal antibody ALK1. Blood 1997, 89:1394 -1404
13. Mason DY, Pulford KA, Bischof D, Kuefer MU, Butler LH, Lamant L, Delsol G, Morris SW: Nucleolar localization of the nucleophosmin-anaplastic lymphoma kinase is not required for malignant transformation. Cancer Res 1998, 58:1057-1062
14. Crockett DK, Lin Z, Elenitoba-Johnson KS, Lim MS: Identification of NPM-ALK interacting proteins by tandem mass spectrometry. Oncogene 2004, 23:2617-2629
15. Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek XM, Polakiewicz RD, Comb MJ: Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 2005, 23:94-101
16. Sachon E, Mohammed S, Bache N, Jensen ON: Phosphopeptide quantitation using amine-reactive isobaric tagging reagents and tandem mass spectrometry: application to proteins isolated by gel electrophoresis. Rapid Commun Mass Spectrom 2006, 20:1127-1134
17. Kånge R, Selditz U, Granberg M, Lindberg U, Ekstrand G, Ek B, Gustafsson M: Comparison of different IMAC techniques used for enrichment of phosphorylated peptides. J Biomol Tech 2005, 16:91-103
18. Stensballe A, Andersen S, Jensen ON: Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off-line mass spectrometry analysis. Proteomics 2001, 1:207-222
19. Bush KD, Lumpkin JA: Structural damage to lactate dehydrogenase during copper iminodiacetic acid metal affinity chromatography. Biotechnol Prog 1998, 14:943-950
20. Ibarrola N, Molina H, Iwahori A, Pandey A: A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine. J Biol Chem 2004, 279:15805-15813
21. Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R: The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4:1985-1988
22. Keller A, Nesvizhskii AI, Kolker E, Aebersold R: Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002, 74:5383-5392
23. Elias JE, Haas W, Faherty BK, Gygi SP: Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2005, 2:667-675
24. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003, 4:R28
25. Feng W, Wang G, Zeeberg BR, Guo K, Fojo AT, Kane DW, Reinhold WC, Lababidi S, Weinstein JN, Wang MD: Development of gene ontology tool for biological interpretation of genomic and proteomic data. AMIA Annu Symp Proc 2003, 839
26. Turner SD, Tooze R, Maclennan K, Alexander DR: Vav-promoter regulated oncogenic fusion protein NPM-ALK in transgenic mice causes B-cell lymphomas with hyperactive Jun kinase. Oncogene 2003, 22:7750-7761
27. Watanabe M, Sasaki M, Itoh K, Higashihara M, Umezawa K, Kadin ME, Abraham LJ, Watanabe T, Horie R: JunB induced by constitutive CD30-extracellular signal-regulated kinase 1/2 mitogen-activated protein kinase signaling activates the CD30 promoter in anaplastic large cell lymphoma and reed-sternberg cells of Hodgkin lymphoma. Cancer Res 2005, 65:7628-7634
28. Slupianek A, Nieborowska-Skorska M, Hoser G, Morrione A, Majewski M, Xue L, Morris SW, Wasik MA, Skorski T: Role of phosphatidyl-inositol 3-kinase-Akt pathway in nucleophosmin/anaplastic lymph-oma kinase-mediated lymphomagenesis. Cancer Res 2001, 61:2194-2199
29. Zhang Q, Raghunath PN, Xue L, Majewski M, Carpentieri DF, Odum N, Morris S, Skorski T, Wasik MA: Multilevel dysregulation of STAT3 activation in anaplastic lymphoma kinase-positive T/null-cell lymphoma. J Immunol 2002, 168:466-474
30. Ouyang T, Bai RY, Bassermann F, von Klitzing C, Klumpen S, Miething C, Morris SW, Peschel C, Duyster J: Identification and characterization of a nuclear interacting partner of anaplastic lymphoma kinase (NIPA). J Biol Chem 2003, 278:30028-30036
31. Brown DJ, Gordon JA: The stimulation of pp60v-src kinase activity by vanadate in intact cells accompanies a new phosphorylation state of the enzyme. J Biol Chem 1984, 259:9580-9586
32. Lemmon MA, Schlessinger J: Regulation of signal transduction and signal diversity by receptor oligomerization. Trends Biochem Sci 1994, 19:459-463
33. Thomas SM, Soriano P, Imamoto A: Specific and redundant roles of Src and Fyn in organizing the cytoskeleton. Nature 1995, 376:267-271