title: Identification of protein biomarkers in Dupuytren's contracture using surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS).
abstract: BACKGROUND
  To study the protein expression profiles associated with Dupuytren's contracture (DC) to identify potential disease protein biomarkers (PBM) using a proteomic technology--Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-TOF-MS).
  
  
  METHODS
  Normal and disease palmar fascia from DC patients were analyzed using Ciphergen's SELDI-TOF-MS Protein Biological System II (PBSII) ProteinChip reader. Analysis of the resulting SELDI-TOF spectra was carried out using the peak cluster analysis program (BioMarker Wizard, Ciphergen). Common peak clusters were then filtered using a bootstrap algorithm called SAM (Significant Analysis of Microarrays) for increased fidelity in our analysis.
  
  
  RESULTS
  Several differentially expressed low molecular weight (<20 kDa) tissue proteins were identified. Spectra generated using both ZipTipC18 aided Au array and WCX2 array based SELDI-TOF-MS were reproducible, with an average peak cluster mass standard deviation for both methods of <1.74 x10(-4). Initial peak cluster analysis of the SELDI spectra identified both up-(14) and down-(3)regulated proteins associated with DC. Further analysis of the peak cluster data using the bootstrap algorithm SAM identified three disease-associated protein features (4600.8 Da, 10254.5 Da, and 11405.1 Da) that were elevated (5.45, 11.7, and 4.28 fold, respectively, with a 0% median false discovery rate).
  
  
  CONCLUSIONS
  SELDI-TOF-MS identified three potential low molecular weight tissue protein markers (p4.6DC, p1ODC, p11.7DC) for DC. The ability of SELDI-TOF-MS to resolve low molecular weight proteins suggests that the method may provide a means of deciphering the biomarker-rich low molecular weight region of the human proteome. Application of such novel technology may help clinicians to focus on specific molecular abnormalities in diseases with no known molecular pathogenesis, and uncover therapeutic and/or diagnostic targets.
authors.affiliation: Cell and Molecular Biology Laboratory, Hand & Upper Limb Centre, University of Western Ontario, London, Canada.
authors.forename: David
authors.initials: D
authors.lastname: O'Gorman
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Howard
authors.forename: Vincenzo M
authors.initials: VM
authors.lastname: Varallo
authors.forename: Peter
authors.initials: P
authors.lastname: Cadieux
authors.forename: Erin
authors.initials: E
authors.lastname: Bowley
authors.forename: Kris
authors.initials: K
authors.lastname: McLean
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Pak
authors.forename: Bing Siang
authors.initials: BS
authors.lastname: Gan
mesh_terms: D000465:Algorithms; D015415:Biomarkers / Q000032:analysis; D004387:Dupuytren Contracture / Q000378:metabolism* / Q000473:pathology; D006801:Humans; D008954:Models, Biological; D008970:Molecular Weight; D040081:Protein Array Analysis / Q000379:methods*; D020543:Proteome / Q000032:analysis; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods* / Q000592:standards
chemical_list: D015415:Biomarkers; D020543:Proteome