Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility

O. John Semmes, Ziding Feng, Bao Ling Adam, Lionel L. Banez, William L. Bigbee, David Campos, Lisa H. Cazares, Daniel W. Chan, William E. Grizzle, Elzbieta Izbicka, Jacob Kagan, Gunjan Malik, Dale McLerran, Judd W. Moul, Alan Partin, Premkala Prasanna, Jason Rosenzweig, Lori J. Sokoll, Shiv Srivastava, Sudhir SrivastavaIan Thompson, Manda J. Welsh, Nicole White, Marcy Winget, Yutaka Yasui, Zhen Zhang, Liu Zhu

Research output: Contribution to journalArticle

300 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)102-112
Number of pages11
JournalClinical Chemistry
Volume51
Issue number1
DOIs
StatePublished - Jan 2005

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Ionization
Mass spectrometry
Blood Proteins
Desorption
Mass Spectrometry
Prostatic Neoplasms
Lasers
Signal-To-Noise Ratio
Serum
Signal to noise ratio
National Cancer Institute (U.S.)
Standardization
Calibration
Assays
Proteins
Research
Neoplasms

ASJC Scopus subject areas

  • Clinical Biochemistry

Cite this

Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer : I. Assessment of platform reproducibility. / Semmes, O. John; Feng, Ziding; Adam, Bao Ling; Banez, Lionel L.; Bigbee, William L.; Campos, David; Cazares, Lisa H.; Chan, Daniel W.; Grizzle, William E.; Izbicka, Elzbieta; Kagan, Jacob; Malik, Gunjan; McLerran, Dale; Moul, Judd W.; Partin, Alan; Prasanna, Premkala; Rosenzweig, Jason; Sokoll, Lori J.; Srivastava, Shiv; Srivastava, Sudhir; Thompson, Ian; Welsh, Manda J.; White, Nicole; Winget, Marcy; Yasui, Yutaka; Zhang, Zhen; Zhu, Liu.

In: Clinical Chemistry, Vol. 51, No. 1, 01.2005, p. 102-112.

Research output: Contribution to journalArticle

Semmes, OJ, Feng, Z, Adam, BL, Banez, LL, Bigbee, WL, Campos, D, Cazares, LH, Chan, DW, Grizzle, WE, Izbicka, E, Kagan, J, Malik, G, McLerran, D, Moul, JW, Partin, A, Prasanna, P, Rosenzweig, J, Sokoll, LJ, Srivastava, S, Srivastava, S, Thompson, I, Welsh, MJ, White, N, Winget, M, Yasui, Y, Zhang, Z & Zhu, L 2005, 'Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility', Clinical Chemistry, vol. 51, no. 1, pp. 102-112. https://doi.org/10.1373/clinchem.2004.038950
Semmes, O. John ; Feng, Ziding ; Adam, Bao Ling ; Banez, Lionel L. ; Bigbee, William L. ; Campos, David ; Cazares, Lisa H. ; Chan, Daniel W. ; Grizzle, William E. ; Izbicka, Elzbieta ; Kagan, Jacob ; Malik, Gunjan ; McLerran, Dale ; Moul, Judd W. ; Partin, Alan ; Prasanna, Premkala ; Rosenzweig, Jason ; Sokoll, Lori J. ; Srivastava, Shiv ; Srivastava, Sudhir ; Thompson, Ian ; Welsh, Manda J. ; White, Nicole ; Winget, Marcy ; Yasui, Yutaka ; Zhang, Zhen ; Zhu, Liu. / Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer : I. Assessment of platform reproducibility. In: Clinical Chemistry. 2005 ; Vol. 51, No. 1. pp. 102-112.
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abstract = "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.",
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T1 - Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer

T2 - I. Assessment of platform reproducibility

AU - Semmes, O. John

AU - Feng, Ziding

AU - Adam, Bao Ling

AU - Banez, Lionel L.

AU - Bigbee, William L.

AU - Campos, David

AU - Cazares, Lisa H.

AU - Chan, Daniel W.

AU - Grizzle, William E.

AU - Izbicka, Elzbieta

AU - Kagan, Jacob

AU - Malik, Gunjan

AU - McLerran, Dale

AU - Moul, Judd W.

AU - Partin, Alan

AU - Prasanna, Premkala

AU - Rosenzweig, Jason

AU - Sokoll, Lori J.

AU - Srivastava, Shiv

AU - Srivastava, Sudhir

AU - Thompson, Ian

AU - Welsh, Manda J.

AU - White, Nicole

AU - Winget, Marcy

AU - Yasui, Yutaka

AU - Zhang, Zhen

AU - Zhu, Liu

PY - 2005/1

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N2 - 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.

AB - 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.

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