title: 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.
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 approximately 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.
authors.affiliation: Department of Microbiology & Molecular Cell Biology, Virginia Prostate Center, Eastern Virginia Medical School, Norfolk, VA 23507, USA. semmesoj@evms.edu
authors.forename: O John
authors.initials: OJ
authors.lastname: Semmes
authors.forename: Ziding
authors.initials: Z
authors.lastname: Feng
authors.forename: Bao-Ling
authors.initials: BL
authors.lastname: Adam
authors.forename: Lionel L
authors.initials: LL
authors.lastname: Banez
authors.forename: William L
authors.initials: WL
authors.lastname: Bigbee
authors.forename: David
authors.initials: D
authors.lastname: Campos
authors.forename: Lisa H
authors.initials: LH
authors.lastname: Cazares
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Chan
authors.forename: William E
authors.initials: WE
authors.lastname: Grizzle
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Izbicka
authors.forename: Jacob
authors.initials: J
authors.lastname: Kagan
authors.forename: Gunjan
authors.initials: G
authors.lastname: Malik
authors.forename: Dale
authors.initials: D
authors.lastname: McLerran
authors.forename: Judd W
authors.initials: JW
authors.lastname: Moul
authors.forename: Alan
authors.initials: A
authors.lastname: Partin
authors.forename: Premkala
authors.initials: P
authors.lastname: Prasanna
authors.forename: Jason
authors.initials: J
authors.lastname: Rosenzweig
authors.forename: Lori J
authors.initials: LJ
authors.lastname: Sokoll
authors.forename: Shiv
authors.initials: S
authors.lastname: Srivastava
authors.forename: Sudhir
authors.initials: S
authors.lastname: Srivastava
authors.forename: Ian
authors.initials: I
authors.lastname: Thompson
authors.forename: Manda J
authors.initials: MJ
authors.lastname: Welsh
authors.forename: Nicole
authors.initials: N
authors.lastname: White
authors.forename: Marcy
authors.initials: M
authors.lastname: Winget
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Yasui
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.forename: Liu
authors.initials: L
authors.lastname: Zhu
mesh_terms: D002138:Calibration; D019411:Clinical Laboratory Techniques / Q000592:standards*; D006801:Humans; D007753:Laboratories / Q000592:standards; D008297:Male; D011471:Prostatic Neoplasms / Q000175:diagnosis*; D040081:Protein Array Analysis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D011786:Quality Control; D015203:Reproducibility of Results; D044967:Serum; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods / Q000592:standards*
chemical_list: D020543:Proteome