MALDI mass spectrometry imaging of formalin-fixed paraffin-embedded tissues in clinical research.

The molecular investigation of archived formalin-fixed, paraffin-embedded (FFPE) tissue samples provides the chance to obtain molecular patterns as indicatives for treatment and clinical end points. MALDI mass spectrometry imaging is capable of localizing molecules like proteins and peptides in tissue sections and became a favorite platform for the targeted and non-targeted approaches, especially in clinical investigations for biomarker research. In FFPE tissues the recovery of proteomic information is constrained by fixation-induced cross-links of proteins. The promising new insights obtained from FFPE in combination with the comprehensive patients' data caused much progress in the optimization of MS imaging protocols to investigate FFPE samples. This review presents the past and current research in MALDI MS imaging of FFPE tissues, demonstrating the improvement of analyses, their actual limitations, but also the promising future perspectives for histopathological and tissue-based research.

[1]  Y. Okada,et al.  Application of Heat-induced Antigen Retrieval to Aldehyde-fixed Fresh Frozen Sections , 2005, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[2]  D. DeVoe,et al.  Proteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens , 2007, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[3]  John A. Kiernan,et al.  Formaldehyde, Formalin, Paraformaldehyde And Glutaraldehyde: What They Are And What They Do , 2000, Microscopy Today.

[4]  T. Veenstra,et al.  Pressure-Assisted Protein Extraction: A Novel Method for Recovering Proteins from Archival Tissue for Proteomic Analysis , 2012, Journal of proteome research.

[5]  G. Murray,et al.  The use of formalin fixed wax embedded tissue for proteomic analysis , 2011, Journal of Clinical Pathology.

[6]  Theodore Alexandrov,et al.  MALDI imaging mass spectrometry: statistical data analysis and current computational challenges , 2012, BMC Bioinformatics.

[7]  Martin Strohalm,et al.  Molecular mass spectrometry imaging in biomedical and life science research , 2010, Histochemistry and Cell Biology.

[8]  M. Setou,et al.  Imaging mass spectrometry of gastric carcinoma in formalin‐fixed paraffin‐embedded tissue microarray , 2010, Cancer science.

[9]  U. Köthe,et al.  Toward digital staining using imaging mass spectrometry and random forests. , 2009, Journal of proteome research.

[10]  Maxence Wisztorski,et al.  MALDI direct analysis and imaging of frozen versus FFPE tissues: what strategy for which sample? , 2010, Methods in molecular biology.

[11]  B. Chait,et al.  Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins. , 1996, Analytical chemistry.

[12]  M. Clench,et al.  MALDI-ion mobility separation-mass spectrometry imaging of glucose-regulated protein 78 kDa (Grp78) in human formalin-fixed, paraffin-embedded pancreatic adenocarcinoma tissue sections. , 2009, Journal of proteome research.

[13]  A. Gown,et al.  Unmasking the mysteries of antigen or epitope retrieval and formalin fixation. , 2004, American journal of clinical pathology.

[14]  M. Clench,et al.  Novel molecular tumour classification using MALDI–mass spectrometry imaging of tissue micro-array , 2010, Analytical and bioanalytical chemistry.

[15]  P. Hudler,et al.  Proteomic Approaches in Biomarker Discovery: New Perspectives in Cancer Diagnostics , 2014, TheScientificWorldJournal.

[16]  R. Caprioli,et al.  Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry. , 2007, Journal of mass spectrometry : JMS.

[17]  J. Roth,et al.  Unconventional antigen retrieval for carbohydrate and protein antigens , 1998, Histochemistry and Cell Biology.

[18]  I. Fournier,et al.  MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting. , 2008, Journal of proteome research.

[19]  G. Siuzdak,et al.  Matrix‐Assisted Laser Desorption/Ionization Mass Spectrometry in Peptide and Protein Analysis , 2006 .

[20]  B. Cillero-Pastor,et al.  Matrix-assisted laser desorption ionization mass spectrometry imaging for peptide and protein analyses: a critical review of on-tissue digestion. , 2014, Journal of proteome research.

[21]  J. Kast,et al.  Advancing formaldehyde cross-linking towards quantitative proteomic applications , 2012, Analytical and Bioanalytical Chemistry.

[22]  P. Quirke,et al.  Detection of the Epidermal Growth Factor Receptor, Amphiregulin and Epiregulin in Formalin-Fixed Paraffin-Embedded Human Placenta Tissue by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging , 2013, European journal of mass spectrometry.

[23]  S. McColl,et al.  Matrix-assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin-fixed tissue. , 2013, Rapid communications in mass spectrometry : RCM.

[24]  P. Selby,et al.  Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. , 2008, Molecular bioSystems.

[25]  Cecilio J. Vidal,et al.  Post-Translational Modifications in Health and Disease , 2011 .

[26]  Peter Hoffmann,et al.  Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues. , 2013, Journal of proteome research.

[27]  Kurt Zatloukal,et al.  Proteomic analysis of PAXgene-fixed tissues. , 2010, Journal of proteome research.

[28]  I. Fournier,et al.  Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections. , 2007, Journal of proteome research.

[29]  M. Clench,et al.  Detergent addition to tryptic digests and ion mobility separation prior to MS/MS improves peptide yield and protein identification for in situ proteomic investigation of frozen and formalin‐fixed paraffin‐embedded adenocarcinoma tissue sections , 2009, Proteomics.

[30]  M. Aubele,et al.  Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. , 2010, Journal of proteome research.

[31]  Bernhard Spengler,et al.  Mass spectrometry imaging with high resolution in mass and space , 2013, Histochemistry and Cell Biology.

[32]  Kristina Schwamborn,et al.  Imaging of Intact Tissue Sections: Moving beyond the Microscope* , 2011, The Journal of Biological Chemistry.

[33]  Theodore Alexandrov,et al.  New analysis workflow for MALDI imaging mass spectrometry: application to the discovery and identification of potential markers of childhood absence epilepsy. , 2012, Journal of proteome research.

[34]  A novel method for analyzing formalin-fixed paraffin embedded (FFPE) tissue sections by mass spectrometry imaging , 2007, Proceedings of the Japan Academy. Series B, Physical and biological sciences.

[35]  M. Clench,et al.  Instrumentation and software for mass spectrometry imaging--making the most of what you've got. , 2012, Journal of proteomics.

[36]  Brendan Prideaux,et al.  Mass spectrometry imaging for drug distribution studies. , 2012, Journal of proteomics.

[37]  Richard M Caprioli,et al.  Imaging Mass Spectrometry—A New and Promising Method to Differentiate Spitz Nevi From Spitzoid Malignant Melanomas , 2012, The American Journal of dermatopathology.

[38]  Sameh Magdeldin,et al.  Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues , 2012, Proteomics.

[39]  Liam A. McDonnell,et al.  Imaging mass spectrometry statistical analysis. , 2012, Journal of proteomics.

[40]  A. Frankel.  Formalin fixation in the ‘‐omics’ era: a primer for the surgeon‐scientist , 2012, ANZ journal of surgery.

[41]  Andrea Urbani,et al.  Protein unlocking procedures of formalin‐fixed paraffin‐embedded tissues: Application to MALDI‐TOF Imaging MS investigations , 2008, Proteomics.

[42]  Pierre P Massion,et al.  High‐throughput proteomic analysis of formalin‐fixed paraffin‐embedded tissue microarrays using MALDI imaging mass spectrometry , 2008, Proteomics.

[43]  P. Kumarathasan,et al.  Current Status and Future Perspectives of Mass Spectrometry Imaging , 2013, International journal of molecular sciences.

[44]  A. Yoshizawa,et al.  Novel In Situ Pretreatment Method for Significantly Enhancing the Signal In MALDI-TOF MS of Formalin-Fixed Paraffin-Embedded Tissue Sections , 2012, PloS one.

[45]  M. Mann,et al.  Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. , 2010, Journal of proteome research.

[46]  Michael Becker,et al.  Tutorial: multivariate statistical treatment of imaging data for clinical biomarker discovery. , 2010, Methods in molecular biology.

[47]  Liam A. McDonnell,et al.  Multiple Statistical Analysis Techniques Corroborate Intratumor Heterogeneity in Imaging Mass Spectrometry Datasets of Myxofibrosarcoma , 2011, PloS one.

[48]  Heinz Höfler,et al.  MALDI imaging mass spectrometry in cancer research: combining proteomic profiling and histological evaluation. , 2013, Clinical biochemistry.

[49]  Peter Hoffmann,et al.  Citric acid antigen retrieval (CAAR) for tryptic peptide imaging directly on archived formalin-fixed paraffin-embedded tissue. , 2010, Journal of proteome research.