title: Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age.
abstract: OBJECTIVE
  Protein profiling of formalin-fixed paraffin-embedded (FFPE) tissues has enormous potential for the discovery and validation of disease biomarkers. The aim of this study was to systematically characterize the effect of length of time of storage of such tissue blocks in pathology archives on the quality of data produced using label-free MS.
  
  
  METHODS
  Normal kidney and clear cell renal cell carcinoma tissues routinely collected up to 10 years prior to analysis were profiled using LC-MS/MS and the data analyzed using MaxQuant. Protein identities and quantification data were analyzed to examine differences between tissue blocks of different ages and assess the impact of technical and biological variability.
  
  
  RESULTS
  An average of over 2000 proteins was seen in each sample with good reproducibility in terms of proteins identified and quantification for normal kidney tissue, with no significant effect of block age. Greater biological variability was apparent in the renal cell carcinoma tissue, possibly reflecting disease heterogeneity, but again there was good correlation between technical replicates and no significant effect of block age.
  
  
  CONCLUSIONS
  These results indicate that archival storage time does not have a detrimental effect on protein profiling of FFPE tissues, supporting the use of such tissues in biomarker discovery studies.
authors.affiliation: Cancer Research UK Centre,, Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, UK.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Craven
authors.forename: David A
authors.initials: DA
authors.lastname: Cairns
authors.forename: Alexandre
authors.initials: A
authors.lastname: Zougman
authors.forename: Patricia
authors.initials: P
authors.lastname: Harnden
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Selby
authors.forename: Rosamonde E
authors.initials: RE
authors.lastname: Banks
mesh_terms: D000328:Adult; D000368:Aged; D015415:Biomarkers / Q000032:analysis*; D014408:Biomarkers, Tumor / Q000032:analysis; D002292:Carcinoma, Renal Cell / Q000737:chemistry; D002853:Chromatography, Liquid; D005260:Female; D005557:Formaldehyde / Q000737:chemistry*; D006801:Humans; D007668:Kidney / Q000737:chemistry*; D007680:Kidney Neoplasms / Q000737:chemistry; D008297:Male; D013058:Mass Spectrometry; D008875:Middle Aged; D016612:Paraffin Embedding / Q000379:methods*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D013997:Time Factors
chemical_list: D015415:Biomarkers; D014408:Biomarkers, Tumor; D020543:Proteome; D005557:Formaldehyde