title: Accessing microenvironment compartments in formalin-fixed paraffin-embedded tissues by protein expression analysis.
abstract: BACKGROUND
  Formalin-fixed paraffin-embedded (FFPE) samples are an outstanding source of new information regarding disease evolvements. Current research on new biomarkers and diseases features has recently invested resources in FFPE-related projects.
  
  
  RESULTS
  In order to initiate clinical protein-expression studies using minute amount of biological material, a workflow based on the combination of filter-assisted sample preparation with MS analysis and label-free quantification was developed. Xenograft lung tumor tissue was investigated as a model system. The workflow was optimized and characterized in terms of its reproducibility from a quantitative and qualitative point of view. We proposed a modification of the original filter-assisted sample preparation protocol to improve reproducibility and highlight its potential for the investigation of hydrophobic proteins.
  
  
  CONCLUSIONS
  Altogether the presented workflow allows analysis of FFPE samples with improvements in the analytical time and performance, and we show its application for lung cancer xenograft tissue samples.
authors.affiliation: Clinical Protein Science & Imaging, Biomedical Center, Department of Measurement Technology & Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Donnarumma
authors.forename: Ákos
authors.initials: Á
authors.lastname: Végvári
authors.forename: Melinda
authors.initials: M
authors.lastname: Rezeli
authors.forename: Charlotte
authors.initials: C
authors.lastname: Welinder
authors.forename: Bo
authors.initials: B
authors.lastname: Jansson
authors.forename: György
authors.initials: G
authors.lastname: Marko-Varga
mesh_terms: D000230:Adenocarcinoma / Q000737:chemistry* / Q000378:metabolism; D000077192:Adenocarcinoma of Lung; D000818:Animals; D014408:Biomarkers, Tumor / Q000032:analysis / Q000096:biosynthesis; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid / Q000379:methods; D005260:Female; D005557:Formaldehyde / Q000737:chemistry; D064593:Heterografts; D006801:Humans; D008175:Lung Neoplasms / Q000737:chemistry* / Q000378:metabolism; D051379:Mice; D016513:Mice, SCID; D009363:Neoplasm Proteins / Q000032:analysis* / Q000096:biosynthesis; D016612:Paraffin Embedding / Q000379:methods*; D051381:Rats; D053719:Tandem Mass Spectrometry / Q000379:methods; D016707:Tissue Fixation / Q000379:methods*; D059016:Tumor Microenvironment
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D005557:Formaldehyde