Evaluation of different two-dimensional chromatographic techniques for proteomic analysis of mouse cardiac tissue

Biomedical Chromatography

Volumn 25, Issue 5, 2011, Pages 594-599

  Callipo, Luciano ^a   Capriotti, Anna Laura ^a   Cavaliere, Chiara ^a   Gubbiotti, Riccardo ^a   Samperi, Roberto ^a   Laganà, Aldo ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Mass spectrometry; Mouse heart; Proteomics; Two dimensional chromatography

Indexed keywords

CHROMATOGRAPHIC ANALYSIS; ELECTROSPRAY IONIZATION; FRACTIONATION; HEART; MAMMALS; MASS SPECTROMETERS; MOLECULAR BIOLOGY; PEPTIDES; TISSUE;

CARDIAC TISSUES; CHROMATOGRAPHIC TECHNIQUES; MOUSE HEART; PROTEIN LEVEL; PROTEOMIC ANALYSIS; PROTEOMICS; REVERSED PHASE; REVERSED PHASE CHROMATOGRAPHY; TWO-DIMENSIONAL; TWO-DIMENSIONAL CHROMATOGRAPHY;

MASS SPECTROMETRY;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; ELECTROSPRAY MASS SPECTROMETRY; EVALUATION; EXTRACTION; HEART; ION EXCHANGE CHROMATOGRAPHY; MALE; MOUSE; NANOTECHNOLOGY; NONHUMAN; PH; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SEPARATION TECHNIQUE; TANDEM MASS SPECTROMETRY;

EID: 79953699348     PISSN: 02693879     EISSN: 10990801     Source Type: Journal    
DOI: 10.1002/bmc.1487     Document Type: Article

References (52)

1. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC and Gygi SP. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Science, USA 2004; 101: 12130-12135.
2. Butt A, Davison MD, Smith GJ, Young JA, Gaskell SJ, Oliver SG and Beynon RJ. Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis. Proteomics 2001; 1: 42-53.
3. Cargile BJ, Talley DL and Stephenson JL Jr. Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides. Electrophoresis 2004; 25: 936-945.
4. Cargile BJ, Sevinsky JR, Essader AS, Stephenson JL Jr and Bundy JL. Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics. Journal of Biomolecular Technology 2005; 16: 181-189.
5. Chen J, Balgley BM, DeVoe DL and Lee CS. Capillary isoelectric focusing-based multidimensional concentration/separation platform for proteome analysis. Analytical Chemistry 2003; 75: 3145-3152.
6. Dai J, Shieh CH, Sheng QH, Zhou H and Zeng R. Proteomic analysis with integrated multiple dimensional liquid chromatography/mass spectrometry based on elution of ion exchange column using pH steps. Analytical Chemistry 2005; 77: 5793-5799.
7. de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Frohlich F, Walther TC and Mann M. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008; 455: 1251-1254.
8. Delmotte N, Lasaosa M, Tholey A, Heinzle E and Huber CG. Two-dimensional reversed-phase × ion-pair reversed-phase hplc: an alternative approach to high-resolution peptide separation for shotgun proteome analysis. Journal of Proteome Research 2007; 6: 4363-4373.
9. Dunn MJ. Two-dimensional polyacrylamide gel electrophoresis for cardiovascular proteomics. Methods in Molecular Biology 2007; 357: 3-13.
10. Essader AS, Cargile BJ, Bundy JL and Stephenson JL Jr. A comparison of immobilized pH gradient isoelectric focusing and strong-cation-exchange chromatography as a first dimension in shotgun proteomics. Proteomics 2005; 5: 24-34.
11. Evans CR and Jorgenson JW. Multidimensional LC-LC and LC-CE for high-resolution separations of biological molecules. Analytical and Bioanalytical Chemistry 2004; 378: 1952-1961.
12. Figeys D, van Oostveen I, Ducret A and Aebersold R. Protein identification by capillary zone electrophoresis/microelectrospray ionization-tandem mass spectrometry at the subfemtomole level. Analytical Chemistry 1996; 68: 1822-1828.
13. Gao J, Opiteck GJ, Friedrichs MS, Dongre AR and Hefta SA. Changes in the protein expression of yeast as a function of carbon source. Journal of Proteome Research 2003; 2: 643-649.
14. Gilar M, Olivova P, Daly AE and Gebler JC. Orthogonality of separation in two-dimensional liquid chromatography. Analytical Chemistry 2005a; 77: 6426-6434.
15. Gilar M, Olivova P, Daly AE and Gebler JC. Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. Journal of Separation Science 2005b; 28: 1694-1703.
16. Giorgianni F, Desiderio DM and Beranova-Giorgianni S. Proteome analysis using isoelectric focusing in immobilized pH gradient gels followed by mass spectrometry. Electrophoresis 2003; 24: 253-259.
17. Gorg A and Weiss W. Analytical IPG-Dalt. Methods in Molecular Biology 1999; 112: 189-195.
18. Gorg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R and Weiss W. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 2000; 21: 1037-1053.
19. Gramolini AO, Kislinger T, Liu P, MacLennan DH and Emili A. Analyzing the cardiac muscle proteome by liquid chromatography-mass spectrometry-based expression proteomics. Methods in Molecular Biology 2007; 357: 15-31.
20. Gygi SP, Corthals GL, Zhang Y, Rochon Y and Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proceedings of the National Academy of Science, USA 2000; 17: 9390-9395.
21. Kachman MT, Wang H, Schwartz DR, Cho KR and Lubman DM. A 2-D Liquid separations/mass mapping method for interlysate comparison of ovarian cancers. Analytical Chemistry 2002; 74: 1779-1791.
22. Krijgsveld J, Gauci S, Dormeyer W and Heck AJ. In-gel isoelectric focusing of peptides as a tool for improved protein identification. Journal of Proteome Research 2006; 5: 1721-1730.
23. Lee CL, Hsiao HH, WLin C, Wu SP, Huang SY, Wu CY, Wang AH and Khoo KH. Strategic shotgun proteomics approach for efficient construction of an expression map of targeted protein families in hepatoma cell lines. Proteomics 2003; 3: 2472-2486.
24. Lee SW, Berger SJ, Martinovic S, PasaTolic L, Anderson GA, Shen Y, Zhao R and Smith RD. Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proceedings of the National Academy of Science, USA 2002; 99: 942-5947.
25. Lemeer S, Pinkse MW, Mohammed S, van Breukelen B, den Hertog J, Slijper M and Heck AJ. Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo. Journal of Proteome Research 2008; 7: 1555-1564.
26. Li W, Hendrickson CL, Emmett MR and Marshall AG. Identification of intact proteins in mixtures by alternated capillary liquid chromatography electrospray ionization and LC ESI infrared multiphoton dissociation fourier transform ion cyclotron resonance mass spectrometry. Analytical Chemistry 1999; 71: 4397-4402.
27. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM and Yates JR. Direct analysis of protein complexes using mass spectrometry. Nature, Biotechnology 1999; 17: 676-682.
28. Marshall J, Jankowski A, Furesz S, Kireeva I, Barker L, Dombrovsky M, Zhu W, Jacks K, Ingratta L, Bruin J, Kristensen E, Zhang R, Stanton E, Takahashi M and Jackowski G. Human serum proteins preseparated by electrophoresis or chromatography followed by tandem mass spectrometry. Journal of Proteome Research 2004; 3: 364-382.
29. Martosella J, Zolotarjova N, Liu H, Nicol G and Boyes BE. Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins. Journal of Proteome Research 2005; 4: 1522-1537.
30. McGregor E and Dunn MJ. Proteomics of the heart: unraveling disease. Circulation Research 2006; 98: 309-321.
31. Nakamura T, Kuromitsu J and Oda Y. Evaluation of comprehensive multidimensional separations using reversed-phase, reversed-phase liquid chromatography/mass spectrometry for shotgun proteomics. Journal of Proteome Research 2008; 7: 1007-1011.
32. Neverova I and Van Eyk JE. Application of reversed phase high performance liquid chromatography for subproteomic analysis of cardiac muscle. Proteomics 2002; 2: 22-31.
33. Olson EN. A decade of discoveries in cardiac biology. Nature, Medicine 2004; 10: 467-474.
34. Opiteck GJ and Jorgenson JW. Two-dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides. Analytical Chemistry 1997; 69: 2283-2291.
35. Peng J, Elias JE, Thoreen CC, Licklider LJ and Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. Journal of Proteome Research 2003; 2: 43-50.
36. Reinders J, Zahedi RP, Pfanner N, Meisinger C and Sickmann A. Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. Journal of Proteome Research 2006; 5: 1543-1554.
37. Shen Y, Jacobs JM, Camp DG, Fang R, Moore RJ, Smith RD, Xiao W, Davis RW and Tompkins RG. Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Analytical Chemistry 2004; 76: 1134-1144.
38. Swanson RV and Glazer AN. Separation of phycobiliprotein subunits by reversed-phase high-pressure liquid chromatography. Analytical Biochemistry 1990; 188: 295-299.
39. Tong W, Link A, Eng JK and Yates JR. Identification of proteins in complexes by solid-phase microextraction/multistep elution/capillary electrophoresis/tandem mass spectrometry. Analytical Chemistry 1999; 71: 2270-2278.
40. Vollmer M, Horth P and Nagele E. Optimization of two-dimensional off-line LC/MS separations to improve resolution of complex proteomic samples. Analytical Chemistry 2004; 76: 5180-5185.
41. Walker AK, Rymar G and Andrews PC. Mass spectrometric imaging of immobilized pH gradient gels and creation of 'virtual' two-dimensional gels. Electrophoresis 2001; 22: 933-945.
42. Wall DB, Kachman MT, Gong S, Hinderer R, Parus S, Misek DE, Hanash SM and Lubman DM. Isoelectric focusing nonporous RP HPLC: a two-dimensional liquid-phase separation method for mapping of cellular proteins with identification using MALDI-TOF mass spectrometry. Analytical Chemistry 2000; 72: 1099-1111.
43. Wang Y, Balgley BM, Rudnick PA and Lee CS. Effects of chromatography conditions on intact protein separations for top-down proteomics. Journal of Chromatography A 2005a; 1073: 35-41.
44. Wang Y, Rudnick PA, Evans EL, Li J, Zhuang Z, Devoe DL, Lee CS and Balgley BM. Proteome analysis of microdissected tumor tissue using a capillary isoelectric focusing-based multidimensional separation platform coupled with ESI-tandem MS. Analytical Chemistry 2005b; 77: 6549-6556.
45. Washburn MP, Wolters D and Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature, Biotechnology 2001; 19: 242-247.
46. Wilson-Grady JT, Villen J and Gygi SP. Phosphoproteome analysis of fission yeast. Journal of Proteome Research 2008; 7: 1088-1097.
47. Wolters DA, Washburn MP and Yates JR. An automated multidimensional protein identification technology for shotgun proteomics. Analytical Chemistry 2001; 73: 5683-5690.
48. Xiao Z, Conrads TP, Lucas DA, Janini GM, Schaefer CF, Buetow KH, Issaq HJ and Veenstra TD. Direct ampholyte-free liquid-phase isoelectric peptide focusing: application to the human serum proteome. Electrophoresis 2004; 25: 128-133.
49. Yan F, Subramanian B, Nakeff A, Barder TJ, Parus SJ and Lubman DM. A comparison of drug-treated and untreated HCT-116 human colon adenocarcinoma cells using a 2-D liquid separation mapping method based upon chromatofocusing PI fractionation. Analytical Chemistry 2003; 75: 2299-2308.
50. Yaneva M and Tempst P. Isolation and mass spectrometry of specific DNA binding proteins. Methods in Molecular Biology 2006; 338: 291-303.
51. Zerkowski HR, Grussenmeyer T, Matt P, Grapow M, Engelhardt S and Lefkovits I. Proteomics strategies in cardiovascular research. Journal of Proteome Research 2004; 3: 200-208.
52. Zolla L and Bianchetti M. High-performance liquid chromatography coupled on-line with electrospray ionization mass spectrometry for the simultaneous separation and identification of the Synechocystis PCC 6803 phycobilisome proteins. Journal of Chromatography A 2001; 912: 269-279.