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Cancer Diagnostics |
1 Department of Microbiology & Molecular Cell Biology, Virginia Prostate Center, Eastern Virginia Medical School, Norfolk, VA.
2 Fred Hutchison Cancer Center, Seattle, WA.
3 Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Rockville, MD.
4 University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA.
5 Cancer Therapy and Research Center, Institute for Drug Development, San Antonio, TX.
6 Department of Pathology, Johns Hopkins Medical Institutes, Baltimore, MD.
7 Department of Pathology, University of Alabama at Birmingham, Birmingham, AL.
8 Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD.
9 Department of Medicine, University of Texas Health Sciences Center, San Antonio, TX.
aAddress correspondence to this author at: Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, 700 W. Olney Rd., Norfolk, VA 23507. Fax 757-446-5766; e-mail semmesoj{at}evms.edu.
Background: Protein expression profiling for differences indicative of early cancer has promise for improving diagnostics. This report describes the first stage of a National Cancer Institute/Early Detection Research Network-sponsored multiinstitutional evaluation and validation of this approach for detection of prostate cancer.
Methods: Two sequential experimental phases were conducted to establish interlaboratory calibration and standardization of the surface-enhanced laser desorption (SELDI) instrumental and assay platform output. We first established whether the output from multiple calibrated Protein Biosystem II SELDI-ionization time-of-flight mass spectrometry (TOF-MS) instruments demonstrated acceptable interlaboratory reproducibility. This was determined by measuring mass accuracy, resolution, signal-to-noise ratio, and normalized intensity of three m/z "peaks" present in a standard pooled serum sample. We next evaluated the ability of the calibrated and standardized instrumentation to accurately differentiate between selected cases of prostate cancer and control by use of an algorithm developed from data derived from a single site 2 years earlier.
Results: When the described standard operating procedures were established at all laboratory sites, the across-laboratory measurements revealed a CV for mass accuracy of 0.1%, signal-to-noise ratio of 
40%, and normalized intensity of 15–36% for the three pooled serum peaks. This was comparable to the intralaboratory measurements of the same peaks. The instrument systems were then challenged with sera from a selected group of 14 cases and 14 controls. The classification agreement between each site and the established decision algorithm were examined by use of both raw peak intensity boosting and ranked peak intensity boosting. All six sites achieved perfect blinded classification for all samples when boosted alignment of raw intensities was used. Four of six sites achieved perfect blinded classification with ranked intensities, with one site passing the criteria of 26 of 28 correct and one site failing with 19 of 28 correct.
Conclusions: These results demonstrate that "between-laboratory" reproducibility of SELDI-TOF-MS serum profiling approaches that of "within-laboratory" reproducibility as determined by measuring discrete m/z peaks over time and across laboratories.
The following articles in journals at HighWire Press have cited this article:
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  C. M. Sturgeon, B. R. Hoffman, D. W. Chan, S.-L. Ch'ng, E. Hammond, D. F. Hayes, L. A. Liotta, E. F. Petricoin, M. Schmitt, O. J. Semmes, et al. National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines for Use of Tumor Markers in Clinical Practice: Quality Requirements Clin. Chem., August 1, 2008; 54(8): e1 - e10. [Abstract] [Full Text] [PDF]
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 J. N. McGuire, J. Overgaard, and F. Pociot Mass spectrometry is only one piece of the puzzle in clinical proteomics Brief Funct Genomic Proteomic, February 28, 2008; (2008) eln005v1. [Abstract] [Full Text] [PDF]
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L. A. Liotta and E. F. Petricoin Putting the "Bio" back into Biomarkers: Orienting Proteomic Discovery toward Biology and away from the Measurement Platform Clin. Chem., January 1, 2008; 54(1): 3 - 5. [Full Text] [PDF]
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R. E. Banks Preanalytical Influences in Clinical Proteomic Studies: Raising Awareness of Fundamental Issues in Sample Banking Clin. Chem., January 1, 2008; 54(1): 6 - 7. [Full Text] [PDF]
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D. McLerran, W. E. Grizzle, Z. Feng, W. L. Bigbee, L. L. Banez, L. H. Cazares, D. W. Chan, J. Diaz, E. Izbicka, J. Kagan, et al. Analytical Validation of Serum Proteomic Profiling for Diagnosis of Prostate Cancer: Sources of Sample Bias Clin. Chem., January 1, 2008; 54(1): 44 - 52. [Abstract] [Full Text] [PDF]
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D. McLerran, W. E. Grizzle, Z. Feng, I. M. Thompson, W. L. Bigbee, L. H. Cazares, D. W. Chan, J. Dahlgren, J. Diaz, J. Kagan, et al. SELDI-TOF MS Whole Serum Proteomic Profiling with IMAC Surface Does Not Reliably Detect Prostate Cancer Clin. Chem., January 1, 2008; 54(1): 53 - 60. [Abstract] [Full Text] [PDF]
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 R. Pelikan, W. L. Bigbee, D. Malehorn, J. Lyons-Weiler, and M. Hauskrecht Intersession reproducibility of mass spectrometry profiles and its effect on accuracy of multivariate classification models Bioinformatics, November 15, 2007; 23(22): 3065 - 3072. [Abstract] [Full Text] [PDF]
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N. Seam, D. A. Gonzales, S. J. Kern, G. L. Hortin, G. T. Hoehn, and A. F. Suffredini Quality Control of Serum Albumin Depletion for Proteomic Analysis Clin. Chem., November 1, 2007; 53(11): 1915 - 1920. [Abstract] [Full Text] [PDF]
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 C. Belluco, E. F. Petricoin, E. Mammano, F. Facchiano, S. Ross-Rucker, D. Nitti, C. Di Maggio, C. Liu, M. Lise, L. A. Liotta, et al. Serum Proteomic Analysis Identifies a Highly Sensitive and Specific Discriminatory Pattern in Stage 1 Breast Cancer Ann. Surg. Oncol., September 1, 2007; 14(9): 2470 - 2476. [Abstract] [Full Text] [PDF]
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R. Machaalani, M. Arlotto, K. A. Waters, E. Gozal, F. Berger, and M. Dematteis A Novel Method of Tissue Collection and Storage: Validation Using SELDI-TOF MS Analysis Clin. Chem., July 1, 2007; 53(7): 1387 - 1389. [Full Text] [PDF]
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J. Albrethsen Reproducibility in Protein Profiling by MALDI-TOF Mass Spectrometry Clin. Chem., May 1, 2007; 53(5): 852 - 858. [Abstract] [Full Text] [PDF]
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 I. M Thompson, M S. Lucia, and C. M Tangen Commentary: The ubiquity of prostate cancer: echoes of the past, implications for the present Int. J. Epidemiol., April 23, 2007; (2007) dym056v1. [Full Text] [PDF]
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 M. Gross, I. Top, I. Laux, J. Katz, J. Curran, C. Tindell, and D. Agus {beta}-2-Microglobulin Is an Androgen-Regulated Secreted Protein Elevated in Serum of Patients with Advanced Prostate Cancer Clin. Cancer Res., April 1, 2007; 13(7): 1979 - 1986. [Abstract] [Full Text] [PDF]
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W. C.S. Cho, T. T.C. Yip, R. K.C. Ngan, T.-T. Yip, V. N. Podust, C. Yip, H. H.Y. Yiu, V. Yip, W.-W. Cheng, V. W.S. Ma, et al. ProteinChip Array Profiling for Identification of Disease- and Chemotherapy-Associated Biomarkers of Nasopharyngeal Carcinoma Clin. Chem., February 1, 2007; 53(2): 241 - 250. [Abstract] [Full Text] [PDF]
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 M. Aivado, D. Spentzos, U. Germing, G. Alterovitz, X.-Y. Meng, F. Grall, A. A. N. Giagounidis, G. Klement, U. Steidl, H. H. Otu, et al. From the cover: Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease PNAS, January 23, 2007; 104(4): 1307 - 1312. [Abstract] [Full Text] [PDF]
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 K. Mosley, F. W. K. Tam, R. J. Edwards, J. Crozier, C. D. Pusey, and L. Lightstone Urinary proteomic profiles distinguish between active and inactive lupus nephritis Rheumatology, December 1, 2006; 45(12): 1497 - 1504. [Abstract] [Full Text] [PDF]
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 D. Nedelkov, U. A. Kiernan, E. E. Niederkofler, K. A. Tubbs, and R. W. Nelson Population Proteomics: The Concept, Attributes, and Potential for Cancer Biomarker Research Mol. Cell. Proteomics, October 1, 2006; 5(10): 1811 - 1818. [Abstract] [Full Text] [PDF]
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R. R. Drake, E. E. Schwegler, G. Malik, J. Diaz, T. Block, A. Mehta, and O. J. Semmes Lectin Capture Strategies Combined with Mass Spectrometry for the Discovery of Serum Glycoprotein Biomarkers Mol. Cell. Proteomics, October 1, 2006; 5(10): 1957 - 1967. [Abstract] [Full Text] [PDF]
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D. S. Cornett, J. A. Mobley, E. C. Dias, M. Andersson, C. L. Arteaga, M. E. Sanders, and R. M. Caprioli A Novel Histology-directed Strategy for MALDI-MS Tissue Profiling That Improves Throughput and Cellular Specificity in Human Breast Cancer Mol. Cell. Proteomics, October 1, 2006; 5(10): 1975 - 1983. [Abstract] [Full Text] [PDF]
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G. L. Hortin The MALDI-TOF Mass Spectrometric View of the Plasma Proteome and Peptidome Clin. Chem., July 1, 2006; 52(7): 1223 - 1237. [Abstract] [Full Text] [PDF]
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G. L. Hortin, S. A. Jortani, J. C. Ritchie Jr, R. Valdes Jr, and D. W. Chan Proteomics: A New Diagnostic Frontier Clin. Chem., July 1, 2006; 52(7): 1218 - 1222. [Abstract] [Full Text] [PDF]
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 E. P. Diamandis Serum Proteomic Profiling by Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry for Cancer Diagnosis: Next Steps Cancer Res., June 1, 2006; 66(11): 5540 - 5541. [Full Text] [PDF]
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 C. Agostini and M. Facco The promising future of proteomics in sarcoidosis. Am. J. Respir. Crit. Care Med., May 15, 2006; 173(10): 1053 - 1054. [Full Text] [PDF]
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E. Kriegova, C. Melle, V. Kolek, B. Hutyrova, F. Mrazek, A. Bleul, R. M. du Bois, F. von Eggeling, and M. Petrek Protein Profiles of Bronchoalveolar Lavage Fluid from Patients with Pulmonary Sarcoidosis Am. J. Respir. Crit. Care Med., May 15, 2006; 173(10): 1145 - 1154. [Abstract] [Full Text] [PDF]
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 A. Jimeno and M. Hidalgo Molecular biomarkers: their increasing role in the diagnosis, characterization, and therapy guidance in pancreatic cancer. Mol. Cancer Ther., April 1, 2006; 5(4): 787 - 796. [Abstract] [Full Text] [PDF]
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 G. Ernst, C. Melle, B. Schimmel, A. Bleul, and F. von Eggeling Proteohistography--Direct Analysis of Tissue with High Sensitivity and High Spatial Resolution Using ProteinChip Technology J. Histochem. Cytochem., January 1, 2006; 54(1): 13 - 17. [Abstract] [Full Text] [PDF]
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S. M. Lin and W. A. Kibbe Irrational Exuberance in Clinical Proteomics Clin. Cancer Res., November 15, 2005; 11(22): 7963 - 7964. [Full Text] [PDF]
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H. W. Ressom, R. S. Varghese, M. Abdel-Hamid, S. A.-L. Eissa, D. Saha, L. Goldman, E. F. Petricoin, T. P. Conrads, T. D. Veenstra, C. A. Loffredo, et al. Analysis of mass spectral serum profiles for biomarker selection Bioinformatics, November 1, 2005; 21(21): 4039 - 4045. [Abstract] [Full Text] [PDF]
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R. E. Banks, A. J. Stanley, D. A. Cairns, J. H. Barrett, P. Clarke, D. Thompson, and P. J. Selby Influences of Blood Sample Processing on Low-Molecular-Weight Proteome Identified by Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry Clin. Chem., September 1, 2005; 51(9): 1637 - 1649. [Abstract] [Full Text] [PDF]
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S. R. Master Diagnostic Proteomics: Back to Basics? Clin. Chem., August 1, 2005; 51(8): 1333 - 1334. [Full Text] [PDF]
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A. Karsan, B. J. Eigl, S. Flibotte, K. Gelmon, P. Switzer, P. Hassell, D. Harrison, J. Law, M. Hayes, M. Stillwell, et al. Analytical and Preanalytical Biases in Serum Proteomic Pattern Analysis for Breast Cancer Diagnosis Clin. Chem., August 1, 2005; 51(8): 1525 - 1528. [Full Text] [PDF]
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N. Jeffries Algorithms for alignment of mass spectrometry proteomic data Bioinformatics, July 15, 2005; 21(14): 3066 - 3073. [Abstract] [Full Text] [PDF]
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 M. Goggins Molecular Markers of Early Pancreatic Cancer J. Clin. Oncol., July 10, 2005; 23(20): 4524 - 4531. [Abstract] [Full Text] [PDF]
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S. Baumann, U. Ceglarek, G. M. Fiedler, J. Lembcke, A. Leichtle, and J. Thiery Standardized Approach to Proteome Profiling of Human Serum Based on Magnetic Bead Separation and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Clin. Chem., June 1, 2005; 51(6): 973 - 980. [Abstract] [Full Text] [PDF]
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 L. A. Liotta, M. Lowenthal, A. Mehta, T. P. Conrads, T. D. Veenstra, D. A. Fishman, and E. F. Petricoin III Importance of Communication Between Producers and Consumers of Publicly Available Experimental Data J Natl Cancer Inst, February 16, 2005; 97(4): 310 - 314. [Abstract] [Full Text] [PDF]
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G. L. Hortin Can Mass Spectrometric Protein Profiling Meet Desired Standards of Clinical Laboratory Practice? Clin. Chem., January 1, 2005; 51(1): 3 - 5. [Full Text] [PDF]
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