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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
Article first published online: 6 MAR 2013
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
PROTEOMICS - Clinical Applications
Special Issue: Proteomic Analysis of Formalin Fixed Tissue
Volume 7, Issue 3-4, pages 273–282, April 2013
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
- Issue published online: 14 APR 2013
- Article first published online: 6 MAR 2013
- Accepted manuscript online: 2 OCT 2012 05:28AM EST
- Manuscript Accepted: 12 SEP 2012
- Manuscript Revised: 4 SEP 2012
- Manuscript Received: 18 JUL 2012
- Cancer Research UK and the Medical Research Council. Grant Number: G0802416
- Label-free MS;
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.
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.
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.