Mass spectrometry-based proteomics and its potential use in haematological research

Archives of Physiology and Biochemistry

Volumn 115, Issue 5, 2009, Pages 286-297

  Fröbel, Julia ^a   Lehr, Stefan ^a   Haas, Rainer ^a   Czibere, Akos ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Haematology; Mass spectrometry; Proteomics

Indexed keywords

PROTEIN; PROTEOME;

ANIMAL; ARTICLE; CHEMISTRY; GENOMICS; HEMATOLOGY; HUMAN; MASS SPECTROMETRY; METHODOLOGY; PROTEOMICS;

ANIMALS; GENOMICS; HEMATOLOGY; HUMANS; MASS SPECTROMETRY; PROTEINS; PROTEOME; PROTEOMICS;

EID: 72049128599     PISSN: 13813455     EISSN: 17444160     Source Type: Journal    
DOI: 10.3109/13813450903428086     Document Type: Article

References (64)

1. Aebersold R, Mann M. (2003). Mass spectrometry-based proteomics. Nature 422(6928):198-207.
2. Aivado M, Spentzos D, Germing U, Alterovitz G , Meng XY, Grall F, Giagounidis AA, Klement G, Steidl U, Otu HH et al. (2005). Optimization and evaluation of surface-enhanced laser desorption/ ionization time-of-flight mass spectrometry (SELDITOF MS) with reversed-phase protein arrays for protein profiling. Clin Chem Lab Med 43(2):133-140
3. Aivado M, Spentzos D, Germing U et al. (2007). Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease. PNAS 104(4):1307-1312
4. Alban A, David SO, Bjorkesten L et al. (2003). A novel experimental design for comparative two-dimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3(1):36-44.
5. Albitar M, Potts SJ, Giles FJ et al. (2009). Proteomics-based prediction of clinical response in acute myeloid leukemia. Exp Hematol 37(7):784-790
6. Amanchy R, Kalume DE, Iwahori A et al. (2005). Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res 4(5):1661-1671
7. Anderson NL, Anderson NG. (2002). The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 1(11):845-867
8. Balogh, MP. (2004). Debating resolution and mass accuracy in mass spectrometry. Spectroscopy 19(10):34-40.
9. Bjellqvist B, Ek K, Righetti PG et al. (1982). Isoelectric focusing in immobilized pH gradients: Principle, methodology and some applications. J Biochem Biophys Methods 6(4):317-339
10. Boernsen KO, Gatzek S, Imbert G. (2005). Controlled protein precipitation in combination with chip-based nanospray infusion mass spectrometry. An approach for metabolomics profiling of plasma. Anal Chem 77(22):7255-7264
11. Charboneau L, Scott H, Chen T et al. (2002). Utility of reverse phase protein arrays: Applications to signalling pathways and human body arrays. Brief Funct Genomic Proteomic 1(3):305-315
12. Chen Y, Jin X, Misek D et al. (1999). Identification of proteins from two-dimensional gel electrophoresis of human erythroleukemia cells using capillary high performance liquid chromatography/electrospray-ion trap-reflectron time-offlight mass spectrometry with two-dimensional topographic map analysis of in-gel tryptic digest products. Rapid Commun Mass Spectrom 13(19):1907-1916
13. Chung CH, Levy S, Chaurand P, Carbone DP. (2007). Genomics and proteomics: Emerging technologies in clinical cancer research. Crit Rev Oncol Hematol 61(1):1-25.
14. Coombes KR, Morris JS, Hu J et al. (2005). Serum proteomics profiling - a young technology begins to mature. Nat Biotechnol 23(3):291-292
15. Cui JW, Wang J, He K et al. (2004). Proteomic analysis of human acute leukemia cells: Insight into their classification. Clin Cancer Res 10(20):6887-6896
16. Czibere A, Grall F, Aivado M (2006). Perspectives of proteomics in acute myeloid leukemia. Expert Rev Anticancer Ther 6(11):1663-1675
17. DePalma A. (2006). Protein profiling poised to make its mark: Understanding which proteins are expressed under which circumstances. GEN 26(1) [online]. Available: http://www. genengnews.com/articles/chitem.aspx?aid= 1209&chid=1 via the Internet. Accessed Jan 1 2006.
18. Diamandis EP. (2004). Analysis of serum proteomic patterns for early cancer diagnosis: Drawing attention to potential problems. J Natl Cancer Inst 96(5):353-356
19. De Francia S, D'Avolio A, De Martino F, Pirro E, Baietto L, Siccardi M, Simiele M, Racca S, Saglio G, Di Carlo F, Di Perri G.(2009). New HPLC-MS method for the simultaneous quantification of the antileukemia drugs imatinib, dasatinib, and nilotinib in human plasma. J Chromatogr B Analyt Technol Biomed Life Sci, 877(18-19): 1721-1726
20. Druker BJ, Tamura S, Buchdunger E et al. (1996). Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med 2(5):561-566
21. Eckel-Passow JE, Oberg AL, Therneau TM. (2009). An insight into high-resolution mass-spectrometry data. Biostatistics 10(3):481-500.
22. Fenn JB, Mann M, Meng CK et al. (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science 246(4926):64-71.
23. Ferrari G, Pastorelli R, Buchi F et al. (2007). Comparative proteomic analysis of chronic myelogenous leukemia cells: Inside the mechanism of imatinib resistance. J Proteome Res 6(1):367-375
24. Fröbel J, Hartwig S, Aivado M et al. (2009). Proteome analysis of platelets from patients with myelodysplastic syndrome shows low expression of proteins required for GPIIb/IIIa function and platelet aggregation. Leuk Res 33(suppl 1):40.
25. Fujii K, Kondo T, Yokoo H et al. (2005). Protein expression pattern distinguishes different lymphoid neoplasms. Proteomics 5(16):4274-4286
26. Gasteiger E, Gattiker A, Hoogland C et al. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31(13):3784-3788
27. Gerber SA, Rush J, Stemman O et al. (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100(12):6940-6945
28. Gygi SP, Rist B, Gerber SA et al. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994-999
29. Han DK, Eng J, Zhou H, Aebersold R (2001). Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 19(10):946-951
30. Hanash SM, Strahler JR, Kuick R et al. (1988). Identification of a polypeptide associated with the malignant phenotype in acute leukemia. J Biol Chem 263(26):12813-12815
31. Haouala A, Zanolari B, Rochat B et al. (2009). Therapeutic drug monitoring of the new targeted anticancer agents imatinib, nilotinib, dasatinib, sunitinib, sorafenib and lapatinib by LC tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 877(22):1982-1996
32. Hartwig S, Czibere A, Kotzka J et al. (2009) Combinatorial hexapeptide ligand libraries (ProteoMiner - - ?). An innovative fractionation tool for differential quantitative clinical proteomics. Arch Physiol Biochem 115(3):155-160
33. Huang H, Stasyk T, Morandell S et al. (2005). Enrichment of lowabundant serum proteins by albumin/immunoglobulin G immunoaffinity depletion under partly denaturing conditions. Electrophoresis 26(14):2843-2849
34. Hutchens TW, Yip TT. (1993). New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun Mass Spectrom 7(7):576-580
35. Ishida Y, Yamashita K, Sasaki H et al. (2008). Activation of complement system in adult T-cell leukemia (ATL) occurs mainly through lectin pathway: A serum proteomic approach using mass spectrometry. Cancer Lett 271(1):167-177
36. Karas M, Hillenkamp F. (1988). Laser desorption ionization of proteins with molecular masses exceeding 10,0 daltons. Anal Chem 60(20):2299-2301
37. Kellermann J. (2008). ICPL - isotope-coded protein label. Methods Mol Biol 424:113-123
38. Kwak J, Tian-Ze M, Yoo M et al. (2004). The comparative analysis of serum proteomes for the discovery of biomarkers for acute myeloid leukemia. Exp Hematol 32(9):836-842
39. Lehr S, Meyer HE. (2009). Integrative proteomics for the future. US HUPO Fifth Annual Conference From Genes to Function held at San Diego, CA, USA, 22-25 February 2009. Proteomics Clin Appl 3(7):756-757
40. Lilley KS, Friedman DB. (2004). All about DIGE: Quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics 1(4):401-409
41. Liu X, Valentine SJ, Plasencia MD et al. (2007). Mapping the human plasma proteome by SCX-LC-IMS-MS. J Am Soc Mass Spectrom 18(7):1249-1264
42. Luo W, Slebos RJ, Hill S et al. (2008). Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res 7(8):3447-3460
43. Marko-Varga G, Fehniger TE (2004). Proteomics and disease - the challenges for technology and discovery. J Proteome Res 3(2):167-178
44. Mohamedali A, Guinn B, Sahu S et al. (2009). Serum profiling reveals distinctive proteomic markers in chronic myeloid leukaemia patients. Br J Haematol 144(2): 362-365
45. O'Farrell PH. (1975). High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250(10):4007-4021
46. Olthoff JK, Lys IA, Cotter RJ (1988). A pulsed time-of-flight mass spectrometer for liquid secondary ion mass spectrometry. Rapid Commun Mass Spectrom 2(9):171-175
47. Parise RA, Egorin MJ, Christner SM et al. (2009). A high-performance liquid chromatography-mass spectrometry assay for quantitation of the tyrosine kinase inhibitor nilotinib in human plasma and serum. J Chromatogr B 877(20-21):1894-1900
48. Paul W, Steinwedel H (1953). Ein neues Massenspektrometer ohne Magnetfeld. Zeitschrift für Naturforschung 8a: 448-450
49. Poirier F, Joubert-Caron R, Labas V, Caron M (2003). Proteomic analysis of a lymphoma-derived cell line (DG75) following treatment with a demethylating drug: Modification of membrane-associated proteins. Proteomics 3(12):1028-1036
50. Rees-Unwin KS, Morgan GJ, Davies FE (2004). Proteomics and the haematologist. Clin Lab Haem 26(2):77-86.
51. Schweigert FJ, Wirth K, Raila J (2004). Characterization of the microheterogeneity of transthyretin in plasma and urine using SELDI-TOF-MS immunoassay. Proteome Sci 2(1):5-11.
52. Scigelova M, Makarov A. (2006). Orbitrap mass analyzer - overview and applications in proteomics. Proteomics 6 (suppl 2): 16-21.
53. Shen Y, Kim J, Strittmatter EF et al. (2005). Characterization of the human blood plasma proteome. Proteomics 5(15):4034-4045 (Pubitemid 41502498)
54. Shi L, Zhang J, Wu P et al. (2009). Discovery and identification of potential biomarkers of pediatric Acute Lymphoblastic Leukemia. Proteome Sci, 7(7) [Online] Available at: http:// www.proteomesci.com/content/7/1/7.
55. Sihlbom C, Kanmert I, von Bahr H, Davidsson P. (2008). Evaluation of the combination of bead technology with SELDI-TOF-MS and 2-D DIGE for detection of plasma proteins. J Proteome Res 7(9):4191-4198
56. Simpson RJ. (2003). Proteins and proteomics: A laboratory manual.Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
57. Steen H, Jebanathirajah JA, Springer M, Kirschner MW. (2005). Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci USA 102(11):3948-3953
58. Thulasiraman V, Lin S, Gheorghiu L et al. (2005). Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis 26:3561-3571
59. Ünlü M, Morgan ME, Minden JS. (1997). Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Electrophoresis 18(11):2071-2077
60. UniProt Consortium. (2009). The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37(Database issue):169-174
61. Unwin RD, Pierce A, Watson RB et al. (2005). Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells. Mol Cell Proteomics 4(7):924-935
62. Wang MC, Papsidero LD, Chu TM (1994). Prostate-specific antigen, p30, gamma-seminoprotein, and E1. Prostate 24(2):107-110
63. Wang W, Zhou H, Lin H et al. (2003). Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75(18):4818-4826
64. Weissinger EM, Schiffer E, Hertenstein B et al. (2007). Proteomic patterns predict acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Blood 109(12):5511-5519