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Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding.
- Source :
-
Proteomics [Proteomics] 2015 Aug; Vol. 15 (15), pp. 2568-79. Date of Electronic Publication: 2015 May 03. - Publication Year :
- 2015
-
Abstract
- Formalin-fixed paraffin-embedded (FFPE) tissue is considered as an appropriate alternative to frozen/fresh tissue for proteomic analysis. Here we study formalin-induced alternations on a proteome-wide level. We compared LC-MS/MS data of FFPE and frozen human kidney tissues by two methods. First, clustering analysis revealed that the biological variation is higher than the variation introduced by the two sample processing techniques and clusters formed in accordance with the biological tissue origin and not with the sample preservation method. Second, we combined open modification search and spectral counting to find modifications that are more abundant in FFPE samples compared to frozen samples. This analysis revealed lysine methylation (+14 Da) as the most frequent modification induced by FFPE preservation. We also detected a slight increase in methylene (+12 Da) and methylol (+30 Da) adducts as well as a putative modification of +58 Da, but they contribute less to the overall modification count. Subsequent SEQUEST analysis and X!Tandem searches of different datasets confirmed these trends. However, the modifications due to FFPE sample processing are a minor disturbance affecting 2-6% of all peptide-spectrum matches and the peptides lists identified in FFPE and frozen tissues are still highly similar.<br /> (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Subjects :
- Amino Acid Sequence
Chromatography, Liquid
Cluster Analysis
Fixatives chemistry
Formaldehyde chemistry
Frozen Sections methods
Humans
Methylation
Proteome classification
Reproducibility of Results
Tandem Mass Spectrometry
Kidney metabolism
Lysine metabolism
Paraffin Embedding methods
Proteome metabolism
Proteomics methods
Tissue Fixation methods
Subjects
Details
- Language :
- English
- ISSN :
- 1615-9861
- Volume :
- 15
- Issue :
- 15
- Database :
- MEDLINE
- Journal :
- Proteomics
- Publication Type :
- Academic Journal
- Accession number :
- 25825003
- Full Text :
- https://doi.org/10.1002/pmic.201400454