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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
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Figure S1. Overlap in proteins identified (A) within each FFPE block age group and (B) between technical replicates in normal kidney cortex and RCC tissue. Overlap in protein identities for normal kidney cortex and RCC tissue are shown within each block age group and between technical replicates.
Tables S1 to S3. MaxQuant data sets generated for normal kidney and RCC tissue samples. Details of the protein groups identified are provided for analysis of 16 samples (4 samples in each of FFPE age groups T1 to T4) of normal kidney cortex (Table 1), technical replicates of each of 2 samples of normal kidney cortex (Table 2) and 8 samples (4 samples in each of FFPE age groups T1 and T4) of RCC tissue plus further technical replicates of 3 samples (Table 3).
Table S4. Correlations for the LC-MS/MS protein quantification between samples within each block age group and between groups for (A) normal renal tissue and (B) RCC tissue. n is the number of pairs and r the Pearson's product moment correlation coefficient in each comparison. Note that normal kidney technical replicates 4.2/.3 and 16.2/.3 were run at the same time as the RCC samples.
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