Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding
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, clu...
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Published in | Proteomics (Weinheim) Vol. 15; no. 15; pp. 2568 - 2579 |
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Main Authors | , , , , , , , , , , , , , |
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01.08.2015
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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. |
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AbstractList | 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. |
Author | Yaoita, Eishin Kinoshita, Naohiko Lisacek, Frederique Yamamoto, Tadashi Yoshida, Yutaka Fujinaka, Hidehiko Muller, Markus Horlacher, Oliver Garessus, Samuel Hasegawa, Miki Xu, Bo Magdeldin, Sameh Nikitin, Frederic Zhang, Ying |
Author_xml | – sequence: 1 givenname: Ying surname: Zhang fullname: Zhang, Ying email: : Dr. Ying Zhang, Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, 8050, Ikarashi 2-no-cho, Nishi-ku, Niigata, Japan 950-2181.: : +81 25 2626925Additional corresponding author: Dr. Markus Muller,, yzhang@med.niigata-u.ac.jpmarkus.mueller@isb-sib.ch organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan – sequence: 2 givenname: Markus surname: Muller fullname: Muller, Markus email: : Dr. Ying Zhang, Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, 8050, Ikarashi 2-no-cho, Nishi-ku, Niigata, Japan 950-2181.: : +81 25 2626925Additional corresponding author: Dr. Markus Muller,, yzhang@med.niigata-u.ac.jpmarkus.mueller@isb-sib.ch organization: SIB-Swiss Institute of Bioinformatics, Geneva, Switzerland – sequence: 3 givenname: Bo surname: Xu fullname: Xu, Bo organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan – sequence: 4 givenname: Yutaka surname: Yoshida fullname: Yoshida, Yutaka organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan – sequence: 5 givenname: Oliver surname: Horlacher fullname: Horlacher, Oliver organization: SIB-Swiss Institute of Bioinformatics, Geneva, Switzerland – sequence: 6 givenname: Frederic surname: Nikitin fullname: Nikitin, Frederic organization: SIB-Swiss Institute of Bioinformatics, Geneva, Switzerland – sequence: 7 givenname: Samuel surname: Garessus fullname: Garessus, Samuel organization: SIB-Swiss Institute of Bioinformatics, Geneva, Switzerland – sequence: 8 givenname: Sameh surname: Magdeldin fullname: Magdeldin, Sameh organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan – sequence: 9 givenname: Naohiko surname: Kinoshita fullname: Kinoshita, Naohiko organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan – sequence: 10 givenname: Hidehiko surname: Fujinaka fullname: Fujinaka, Hidehiko organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan – sequence: 11 givenname: Eishin surname: Yaoita fullname: Yaoita, Eishin organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan – sequence: 12 givenname: Miki surname: Hasegawa fullname: Hasegawa, Miki organization: Division of Digestive & General Surgery, Niigata University, Niigata, Japan – sequence: 13 givenname: Frederique surname: Lisacek fullname: Lisacek, Frederique organization: SIB-Swiss Institute of Bioinformatics, Geneva, Switzerland – sequence: 14 givenname: Tadashi surname: Yamamoto fullname: Yamamoto, Tadashi organization: Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan |
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Keywords | FFPE tissue Open modification search Lysine methylation Spectral library Bioinformatics |
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Snippet | Formalin‐fixed paraffin‐embedded (FFPE) tissue is considered as an appropriate alternative to frozen/fresh tissue for proteomic analysis. Here we study... Formalin-fixed paraffin-embedded (FFPE) tissue is considered as an appropriate alternative to frozen/fresh tissue for proteomic analysis. Here we study... |
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SubjectTerms | Amino Acid Sequence Bioinformatics Chromatography, Liquid Cluster Analysis FFPE tissue Fixatives - chemistry Formaldehyde - chemistry Frozen Sections - methods Humans Kidney - metabolism Lysine - metabolism Lysine methylation Methylation Open modification search Paraffin Embedding - methods Proteome - classification Proteome - metabolism Proteomics - methods Reproducibility of Results Spectral library Tandem Mass Spectrometry Tissue Fixation - methods |
Title | Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding |
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