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Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry
Open accessAbstract
Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE-TMAs using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE-TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis.
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Citations
Cites
Tissue microarrays for high-throughput molecular profiling of tumor specimens
Kononen, J., Bubendorf, L., Kallionimeni, A., Bärlund, M., Schraml, P., Leighton, S., Torhorst, J., Mihatsch, M. J., Sauter, G., & Kallionimeni, O.-P. (1998) · Nature Medicine · doi:10.1038/nm0798-844 · Cited by 4,099
Shi, S. R., Key, M. E., & Kalra, K. L. (1991) · Journal of Histochemistry & Cytochemistry · doi:10.1177/39.6.1709656 · Cited by 2,552
Going deeper than microscopy: the optical imaging frontier in biology
Ntziachristos, V. (2010) · Nature Methods · doi:10.1038/nmeth.1483 · Cited by 1,896
Analysis of Proteins and Proteomes by Mass Spectrometry
Mann, M., Hendrickson, R. C., & Pandey, A. (2001) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.70.1.437 · Cited by 1,219
Schwartz, S. A., Reyzer, M. L., & Caprioli, R. M. (2003) · Journal of Mass Spectrometry · doi:10.1002/jms.505 · Cited by 646
Self-citationEffect of formalin tissue fixation and processing on immunohistochemistry
Werner, M., Chott, A., Fabiano, A., & Battifora, H. (2000) · The American Journal of Surgical Pathology · doi:10.1097/00000478-200007000-00014 · Cited by 598
High-throughput fluorescence microscopy for systems biology
Pepperkok, R., & Ellenberg, J. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1979 · Cited by 412
Groseclose, M. R., Andersson, M., Hardesty, W. M., & Caprioli, R. M. (2007) · Journal of Mass Spectrometry · doi:10.1002/jms.1177 · Cited by 377
Self-citationIntegrating Histology and Imaging Mass Spectrometry
Chaurand, P., Schwartz, S. A., Billheimer, D., Xu, B. J., Crecelius, A., & Caprioli, R. M. (2004) · Analytical Chemistry · doi:10.1021/ac0351264 · Cited by 365
Self-citationAutomated Acoustic Matrix Deposition for MALDI Sample Preparation
Aerni, H.-R., Cornett, D. S., & Caprioli, R. M. (2006) · Analytical Chemistry · doi:10.1021/ac051534r · Cited by 344
Self-citationMALDI-FTICR Imaging Mass Spectrometry of Drugs and Metabolites in Tissue
Cornett, D. S., Frappier, S. L., & Caprioli, R. M. (2008) · Analytical Chemistry · doi:10.1021/ac800617s · Cited by 343
Self-citationAntigen Retrieval Techniques: Current Perspectives
Shi, S.-R., Cote, R. J., & Taylor, C. R. (2001) · Journal of Histochemistry & Cytochemistry · doi:10.1177/002215540104900801 · Cited by 335
Groseclose, M. R., Massion, P. P., Chaurand, P., & Caprioli, R. M. (2008) · PROTEOMICS · doi:10.1002/pmic.200800495 · Cited by 319
Self-citationDirect Analysis and MALDI Imaging of Formalin-Fixed, Paraffin-Embedded Tissue Sections
Lemaire, R., Desmons, A., Tabet, J. C., Day, R., Salzet, M., & Fournier, I. (2007) · Journal of Proteome Research · doi:10.1021/pr060549i · Cited by 309
Molecular imaging of proteins in tissues by mass spectrometry
Seeley, E. H., & Caprioli, R. M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801374105 · Cited by 303
Self-citationAntibody-based Proteomics for Human Tissue Profiling
Uhlen, M., & Ponten, F. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500009-mcp200 · Cited by 303
Shi, S., Shi, Y., & Taylor, C. R. (2011) · Journal of Histochemistry & Cytochemistry · doi:10.1369/jhc.2010.957191 · Cited by 280
MALDI-MS-based imaging of small molecules and proteins in tissues
Reyzer, M. L., & Caprioli, R. M. (2007) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2006.11.035 · Cited by 228
Self-citationShi, S.-R., Liu, C., Balgley, B. M., Lee, C., & Taylor, C. R. (2006) · Journal of Histochemistry & Cytochemistry · doi:10.1369/jhc.5b6851.2006 · Cited by 225
Processing MALDI mass spectra to improve mass spectral direct tissue analysis
Norris, J. L., Cornett, D. S., Mobley, J. A., Andersson, M., Seeley, E. H., Chaurand, P., & Caprioli, R. M. (2007) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2006.10.005 · Cited by 220
Self-citationNilsson, A., Fehniger, T. E., Gustavsson, L., Andersson, M., Kenne, K., Marko-Varga, G., & Andrén, P. E. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011411 · Cited by 215
Automated MALDI Matrix Deposition Method with Inkjet Printing for Imaging Mass Spectrometry
Baluya, D. L., Garrett, T. J., & Yost, R. A. (2007) · Analytical Chemistry · doi:10.1021/ac070958d · Cited by 202
Identification of Formaldehyde-Induced Modifications in Proteins: Reactions with Insulin
Metz, B., Kersten, G. F. A., Baart, G. J. E., de Jong, A., Meiring, H., ten Hove, J., van Steenbergen, M. J., Hennink, W. E., Crommelin, D. J. A., & Jiskoot, W. (2006) · Bioconjugate Chemistry · doi:10.1021/bc050340f · Cited by 183
Heat-induced antigen retrieval: Mechanisms and application to histochemistry
Yamashita, S. (2007) · Progress in Histochemistry and Cytochemistry · doi:10.1016/j.proghi.2006.09.001 · Cited by 177
Identifying prostate carcinoma by MALDI-Imaging
Schwamborn, K., Krieg, R., Reska, M., Jakse, G., Knuechel, R., & Wellmann, A. (2007) · International Journal of Molecular Medicine · doi:10.3892/ijmm.20.2.155 · Cited by 168
Optimizing UV laser focus profiles for improved MALDI performance
Holle, A., Haase, A., Kayser, M., & Höhndorf, J. (2006) · Journal of Mass Spectrometry · doi:10.1002/jms.1041 · Cited by 167
Taylor, C. R., Shi, S., Chen, C., Young, L. L., Yang, C. J., & Côté, R. J. (1996) · Biotechnic & Histochemistry · doi:10.3109/10520299609117171 · Cited by 146
Novel molecular tumour classification using MALDI–mass spectrometry imaging of tissue micro-array
Djidja, M., Claude, E., Snel, M. F., Francese, S., Scriven, P., Carolan, V. A., & Clench, M. R. (2010) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-010-3554-6 · Cited by 129
MALDI Imaging Mass Spectrometry – Painting Molecular Pictures
Schwamborn, K., & Caprioli, R. M. (2010) · Molecular Oncology · doi:10.1016/j.molonc.2010.09.002 · Cited by 129
Self-citationMALDI Imaging Mass Spectrometry of Integral Membrane Proteins from Ocular Lens and Retinal Tissue
Grey, A. C., Chaurand, P., Caprioli, R. M., & Schey, K. L. (2009) · Journal of Proteome Research · doi:10.1021/pr800956y · Cited by 111
Self-citationIn vivo imaging in experimental preclinical tumor research–A review
Wessels, J. T., Busse, A. C., Mahrt, J., Dullin, C., Grabbe, E., & Mueller, G. (2007) · Cytometry Part A · doi:10.1002/cyto.a.20419 · Cited by 98
Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges
Nirmalan, N. J., Harnden, P., Selby, P. J., & Banks, R. E. (2008) · Molecular BioSystems · doi:10.1039/b800098k · Cited by 88
Verification of automated peptide identifications from proteomic tandem mass spectra
Tabb, D. L., Friedman, D. B., & Ham, A. L. (2006) · Nature Protocols · doi:10.1038/nprot.2006.330 · Cited by 57
Yang, Y., Xu, Y., Kersten, R. D., Liu, W., Meehan, M. J., Moore, B. S., Bandeira, N., & Dorrestein, P. C. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201101225 · Cited by 56
Immunohistology—Past, Present, and Future
Leong, T. Y.-M., Cooper, K., & Leong, A. S. ‐. (2010) · Advances in Anatomic Pathology · doi:10.1097/pap.0b013e3181f8957c · Cited by 54
Antigen Retrieval in Formaldehyde-Fixed Human Brain Tissue
Evers, P., Uylings, H. B. M., & Suurmeijer, A. J. H. (1998) · Methods · doi:10.1006/meth.1998.0616 · Cited by 40
The Immunohistochemistry Laboratory: Looking at Molecules and Preparing for Tomorrow
Teruya‐Feldstein, J. (2010) · Archives of Pathology & Laboratory Medicine · doi:10.5858/2009-0582-rar1.1 · Cited by 31
Antigen Retrieval in Immunohistochemistry
Shi, S. R., & Taylor, C. R. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-386456-7.07404-9 · Cited by 20
Demonstration of amyloid protein AA in old museum specimens.
Westermark, P., & Gt, N. (1984) · PubMed · Cited by 20
Aerni, H. R., Cornett, D. S., & Caprioli, R. M. (2009) · Analytical Chemistry · doi:10.1021/ac900974j · Cited by 18
Self-citationProteomic analysis and classification of metastatic melanoma by MALDI imaging mass spectrometry
Hardesty, W. M. (2010) · Cited by 2
Cited by
Körber, A., Anthony, I. G. M., & Heeren, R. M. A. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c05249 · Cited by 88
Metadata
- Authors
- Casadonte, R., & Caprioli, R. M.
- Venue
- Nature Protocols
- Published
- 2011-10-13
- Volume
- 6
- Issue
- 11
- Pages
- 1695-1709
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W2027375922
- Cited by
- 279
- References
- 41
- FWCI
- 9.85
- Type
- journal article
- Language
- en
- Open access
- green
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