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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

  1. Rachel A. Craven1,
  2. David A. Cairns1,
  3. Alexandre Zougman1,
  4. Patricia Harnden1,2,
  5. Peter J. Selby1,
  6. Rosamonde E. Banks1,*

Article first published online: 6 MAR 2013

DOI: 10.1002/prca.201200065

Issue

PROTEOMICS - Clinical Applications

PROTEOMICS - Clinical Applications

Special Issue: Proteomic Analysis of Formalin Fixed Tissue

Volume 7, Issue 3-4, pages 273–282, April 2013

Additional Information

How to Cite

Craven, R. A., Cairns, D. A., Zougman, A., Harnden, P., Selby, P. J. and Banks, R. E. (2013), 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. Prot. Clin. Appl., 7: 273–282. doi: 10.1002/prca.201200065

Author Information

  1. 1

    Cancer Research UK Centre,, Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, UK

  2. 2

    Department of Histopathology,, St. James's University Hospital, Leeds, UK

* Correspondence: Professor Rosamonde E. Banks, Cancer Research UK Centre, Leeds Institute of Molecular Medicine, St. James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
E-mail: r.banks@leeds.ac.uk
Fax: +44-113-2429886

  1. Colour Online: See the article online to view Figs. 1 and 4 in colour.

Publication History

  1. Issue published online: 14 APR 2013
  2. Article first published online: 6 MAR 2013
  3. Accepted manuscript online: 2 OCT 2012 05:28AM EST
  4. Manuscript Accepted: 12 SEP 2012
  5. Manuscript Revised: 4 SEP 2012
  6. Manuscript Received: 18 JUL 2012

Funded by

  • Cancer Research UK and the Medical Research Council. Grant Number: G0802416

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Keywords:

  • FFPE;
  • Kidney;
  • Label-free MS;
  • Pre-analytical;
  • RCC

Purpose

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.

Experimental design

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 and clinical relevance

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.

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