Seminars in Nephrology
Volume 27, Issue 6 , Pages 597-608 , November 2007

Direct Tissue Analysis by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry: Application to Kidney Biology

  • Kristen D. Herring

      Affiliations

    • Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN.
    • ,
  • Stacey R. Oppenheimer, PhD

      Affiliations

    • Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN.
    • ,
  • Richard M. Caprioli, PhD

      Affiliations

    • Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN.
    • Corresponding Author InformationAddress reprint requests to Richard M. Caprioli, Vanderbilt University, 9160 Medical Research Bldg III, 465 21st Ave S, Nashville, TN 37232-8575.

References 

  1. Hillenkamp F, Karas M, Beavis RC, Chait BT. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal Chem. 1991;63:1193A–1203A
  2. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem. 1988;60:2299–2301
  3. Chaurand P, Caprioli RM. Direct profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry. Electrophoresis. 2002;23:3125–3135
  4. Schwartz SA, Reyzer ML, Caprioli RM. Direct tissue analysis using matrix-assisted laser desorption/ionization mass spectrometry: practical aspects of sample preparation. J Mass Spectrom. 2003;38:699–708
  5. Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem. 1997;69:4751–4760
  6. Karas M, Gluckmann M, Schafer J. Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors. J Mass Spectrom. 2000;35:1–12
  7. Zenobi R, Knochenmuss R. Ion formation in MALDI mass spectrometry. Mass Spectrom Rev. 1998;17:337-6
  8. Wiley WC, McLaren IH. Time-of-flight mass spectrometer with improved resolution. Rev Sci Instruments. 1955;26:1150–1157
  9. Cotter RJ. The new time-of-flight mass spectrometry. Anal Chem. 1999;71:445A–451A
  10. Khatib-Shahidi S, Andersson M, Herman JL, Gillespie TA, Caprioli RM. Direct molecular analysis of whole-body animal tissue sections by imaging MALDI mass spectrometry. Anal Chem. 2006;78:6448–6456
  11. Reyzer ML, Caprioli RM. MALDI-MS-based imaging of small molecules and proteins in tissues. Curr Opin Chem Biol. 2007;11:29–35
  12. Troendle FJ, Reddick CD, Yost RA. Detection of pharmaceutical compounds in tissue by matrix-assisted laser desorption/ionization and laser desorption/chemical ionization tandem mass spectrometry with a quadrapole ion trap. J Am Soc Mass Spectrom. 1999;10:1315–1321
  13. Reyzer ML, Hsieh Y, Ng K, Korfmacher WA, Caprioli RM. Direct analysis of drug candidates in tissue by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom. 2003;38:1081–1092
  14. Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat Med. 2001;7:493–496
  15. Chaurand P, Cornett DS, Caprioli RM. Molecular imaging of thin mammalian tissue sections by mass spectrometry. Curr Opin Biotechnol. 2006;17:431–436
  16. Schwartz SA, Weil RJ, Johnson MD, Toms SA, Caprioli RM. Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression. Clin Cancer Res. 2004;10:981–987
  17. Schwartz SA, Weil RJ, Thompson RC, Shyr Y, Moore JH, Toms SA, et al. Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry. Cancer Res. 2005;65:7674–7681
  18. Srinivasan M, Sedmak D, Jewell S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol. 2002;161:1961–1971
  19. Aerni HR, Cornett DS, Caprioli RM. Automated acoustic matrix deposition for MALDI sample preparation. Anal Chem. 2006;78:827–834
  20. Xu BJ, Caprioli RM, Sanders ME, Jensen RA. Direct analysis of laser capture microdissected cells by MALDI mass spectrometry. J Am Soc Mass Spectrom. 2002;13:1292–1297
  21. Cornett DS, Mobley JA, Dias EC, Andersson M, Arteaga CL, Sanders ME, et al. A novel histology-directed strategy for MALDI-MS tissue profiling that improves throughput and cellular specificity in human breast cancer. Mol Cell Proteomics. 2006;5:1975–1983
  22. Groseclose MR, Andersson M, Hardesty WM, Caprioli RM. Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry. J Mass Spectrom. 2007;42:254–262
  23. Chaurand P, Schwartz SA, Billheimer D, Xu BJ, Crecelius A, Caprioli RM. Integrating histology and imaging mass spectrometry. Anal Chem. 2004;76:1145–1155
  24. Norris JL, Cornett DS, Mobley JA, Andersson M, Seeley EH, Chaurand P, et al. Processing MALDI mass spectra to aid biomarker discovery and improve mass spectral image quality. Int J Mass Spectrom. 2007;260:212–221
  25. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response (vol 98, pg 5116, 2001). Proc Natl Acad Sci U S A. 2001;98:10515
  26. Naiman DQ. Random data set generation to support microarray analysis. Methods Enzymol. 2006;411:312–325
  27. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, et al. Gene-expression profiles in hereditary breast cancer. N Engl J Med. 2001;344:539–548
  28. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003;100:9440–9445
  29. Reid GE, McLuckey SA. ‘Top down’ protein characterization via tandem mass spectrometry. J Mass Spectrom. 2002;37:663–675
  30. Wysocki VH, Resing KA, Zhang Q, Cheng G. Mass spectrometry of peptides and proteins. Methods. 2005;35:211–222
  31. Hirosawa M, Hoshida M, Ishikawa M, Toya T. MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming. Comput Appl Biosci. 1993;9:161–167
  32. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, et al. Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol. 1999;17:676–682
  33. Ponticelli C, Villa M, Banfi G, Cesana B, Pozzi C, Pani A, et al. Can prolonged treatment improve the prognosis in adults with focal segmental glomerulosclerosis?. Am J Kidney Dis. 1999;34:618–625
  34. Xu BJ, Shyr Y, Liang X, Ma LJ, Donnert EM, Roberts JD, et al. Proteomic patterns and prediction of glomerulosclerosis and its mechanisms. J Am Soc Nephrol. 2005;16:2967–2975
  35. Meistermann H, Norris JL, Aerni HR, Cornett DS, Friedlein A, Erskine AR, et al. Biomarker discovery by imaging mass spectrometry: transthyretin is a biomarker for gentamicin-induced nephrotoxicity in rat. Mol Cell Proteomics. 2006;5:1876–1886
  36. Bernstein LH, Ingenbleek Y. Transthyretin: its response to malnutrition and stress injury (Clinical usefulness and economic implications). Clin Chem Lab Med. 2002;40:1344–1348
  37. Ingenbleek Y, Young V. Transthyretin (prealbumin) in health and disease: nutritional implications. Annu Rev Nutr. 1994;14:495–533
  38. Lasztity N, Biro L, Nemeth E, Pap A, Antal M. Protein status in pancreatitis—transthyretin is a sensitive biomarker of malnutrition in acute and chronic pancreatitis. Clin Chem Lab Med. 2002;40:1320–1324
  39. Sousa MM, Norden AG, Jacobsen C, Willnow TE, Christensen EI, Thakker RV, et al. Evidence for the role of megalin in renal uptake of transthyretin. J Biol Chem. 2000;275:38176–38181
  40. Verroust PJ, Birn H, Nielsen R, Kozyraki R, Christensen EI. The tandem endocytic receptors megalin and cubilin are important proteins in renal pathology. Kidney Int. 2002;62:745–756
  41. Moestrup SK, Cui S, Vorum H, Bregengard C, Bjorn SE, Norris K, et al. Evidence that epithelial glycoprotein 330/megalin mediates uptake of polybasic drugs. J Clin Invest. 1995;96:1404–1413
  42. Balch GC, Mithani SK, Simpson JF, Kelley MC. Accuracy of intraoperative gross examination of surgical margin status in women undergoing partial mastectomy for breast malignancy. Am Surg. 2005;71:22–28
  43. Looser KG, Shah JP, Strong EW. The significance of “positive” margins in surgically resected epidermoid carcinomas. Head Neck Surg. 1978;1:107–111
  44. Nathan CO, Amirghahri N, Rice C, Abreo FW, Shi R, Stucker FJ. Molecular analysis of surgical margins in head and neck squamous cell carcinoma patients. Laryngoscope. 2002;112:2129–2140
  45. Dechet CB, Zincke H, Sebo TJ, King BF, LeRoy AJ, Farrow GM, et al. Prospective analysis of computerized tomography and needle biopsy with permanent sectioning to determine the nature of solid renal masses in adults. J Urol. 2003;169:71–74
  46. Nguyen TT, Parkinson JP, Kuehn DM, Winfield HN. Technique for ensuring negative surgical margins during laparoscopic partial nephrectomy. J Endourol. 2005;19:410–415
  47. Sengupta S, Zincke H. Lessons learned in the surgical management of renal cell carcinoma. Urology. 2005;66:36–42
  48. Acker T, Fandrey J, Acker H. The good, the bad and the ugly in oxygen-sensing: ROS, cytochromes and prolyl-hydroxylases. Cardiovasc Res. 2006;71:195–207
  49. Gatenby RA, Gawlinski ET. The glycolytic phenotype in carcinogenesis and tumor invasion: insights through mathematical models. Cancer Res. 2003;63:3847–3854
  50. Giaccia AJ, Simon MC, Johnson R. The biology of hypoxia: the role of oxygen sensing in development, normal function, and disease. Genes Dev. 2004;18:2183–2194
  51. Guzy RD, Schumacker PT. Oxygen sensing by mitochondria at complex III: the paradox of increased reactive oxygen species during hypoxia. Exp Physiol. 2006;91:807–819
  52. Haase VH. The VHL/HIF oxygen-sensing pathway and its relevance to kidney disease. Kidney Int. 2006;69:1302–1307
  53. Hervouet E, Demont J, Pecina P, Vojtiskova A, Houstek J, Simonnet H, et al. A new role for the von Hippel-Lindau tumor suppressor protein: stimulation of mitochondrial oxidative phosphorylation complex biogenesis. Carcinogenesis. 2005;26:531–539
  54. Raghunand N, Gatenby RA, Gillies RJ. Microenvironmental and cellular consequences of altered blood flow in tumours. Br J Radiol. 2003;76:S11–S22
  55. Simonnet H, Alazard N, Pfeiffer K, Gallou C, Beroud C, Demont J, et al. Low mitochondrial respiratory chain content correlates with tumor aggressiveness in renal cell carcinoma. Carcinogenesis. 2002;23:759–768
  56. Warburg O. The metabolism of tumors. London: Constable Press; 1930;

 Supported in part by National Institutes of Health/National Institute of General Medical Sciences (NIGMS) GMS8008-08.

PII: S0270-9295(07)00124-6

doi: 10.1016/j.semnephrol.2007.09.002

Seminars in Nephrology
Volume 27, Issue 6 , Pages 597-608 , November 2007

Article Tools

* Image Usage & Resolution