title: LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis.
abstract: BACKGROUND
  Melanoma metastasis status is highly associated with the overall survival of patients; yet, little is known about proteomic changes during melanoma tumor progression. To better understand the changes in protein expression involved in melanoma progression and metastasis, and to identify potential biomarkers, we conducted a global quantitative proteomic analysis on archival metastatic and primary melanomas.
  
  
  RESULTS
  A total of 16 metastatic and 8 primary cutaneous melanomas were assessed. Proteins were extracted from laser captured microdissected formalin fixed paraffin-embedded archival tissues by liquefying tissue cells. These preparations were analyzed by a LC/MS-based label-free protein quantification method. More than 1500 proteins were identified in the tissue lysates with a peptide ID confidence level of >75%. This approach identified 120 significant changes in protein levels. These proteins were identified from multiple peptides with high confidence identification and were expressed at significantly different levels in metastases as compared with primary melanomas (q-Value<0.05).
  
  
  CONCLUSIONS
  The differentially expressed proteins were classified by biological process or mapped into biological system networks, and several proteins were implicated by these analyses as cancer- or metastasis-related. These proteins represent potential biomarkers for tumor progression. The study successfully identified proteins that are differentially expressed in formalin fixed paraffin-embedded specimens of metastatic and primary melanoma.
authors.affiliation: Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America.
authors.forename: Sharon K
authors.initials: SK
authors.lastname: Huang
authors.forename: Marlene M
authors.initials: MM
authors.lastname: Darfler
authors.forename: Michael B
authors.initials: MB
authors.lastname: Nicholl
authors.forename: Jinsam
authors.initials: J
authors.lastname: You
authors.forename: Kerry G
authors.initials: KG
authors.lastname: Bemis
authors.forename: Tony J
authors.initials: TJ
authors.lastname: Tegeler
authors.forename: Mu
authors.initials: M
authors.lastname: Wang
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Wery
authors.forename: Kelly K
authors.initials: KK
authors.lastname: Chong
authors.forename: Linhda
authors.initials: L
authors.lastname: Nguyen
authors.forename: Richard A
authors.initials: RA
authors.lastname: Scolyer
authors.forename: Dave S B
authors.initials: DS
authors.lastname: Hoon
mesh_terms: D000818:Animals; D014408:Biomarkers, Tumor / Q000032:analysis*; D002853:Chromatography, Liquid / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D008545:Melanoma / Q000737:chemistry / Q000473:pathology; D008969:Molecular Sequence Data; D009362:Neoplasm Metastasis; D009363:Neoplasm Proteins / Q000032:analysis*; D016612:Paraffin Embedding; D020543:Proteome / Q000032:analysis*
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome