Direct Analysis and MALDI Imaging of Formalin-Fixed, Paraffin-Embedded Tissue Sections

Formalin fixation, generally followed by paraffin embedding, is the standard and well-established processing method employed by pathologist. This treatment conserves and stabilizes biopsy samples for years. Analysis of FFPE tissues from biopsy libraries has been, so far, a challenge for proteomics b...

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Bibliographic Details
Published in:Journal of proteome research 2007-04, Vol.6 (4), p.1295-1305
Main Authors: Lemaire, R, Desmons, A, Tabet, J. C, Day, R, Salzet, M, Fournier, I
Format: Article
Language:English
Subjects:
Animals
Brain Chemistry
Formaldehyde - chemistry
Humans
Microtomy
Paraffin Embedding
Proteins - analysis
Proteomics - methods
Rats
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods
Tissue Fixation
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Summary:Formalin fixation, generally followed by paraffin embedding, is the standard and well-established processing method employed by pathologist. This treatment conserves and stabilizes biopsy samples for years. Analysis of FFPE tissues from biopsy libraries has been, so far, a challenge for proteomics biomarker studies. Herein, we present two methods for the direct analysis of formalin-fixed, paraffin-embedded (FFPE) tissues by MALDI−MS. The first is based on the use of a reactive matrix, 2,4-dinitrophenylhydrazine, useful for FFPE tissues stored less than 1 year. The second approach is applicable for all FFPE tissues regardless of conservation time. The strategy is based on in situ enzymatic digestion of the tissue section after paraffin removal. In situ digestion can be performed on a specific area of the tissue as well as on a very small area (microdigestion). Combining automated microdigestion of a predefined tissue array with either in situ extraction prior to classical nanoLC/MS−MS analysis or automated microspotting of MALDI matrix according to the same array allows the identification of both proteins by nanoLC-nanoESI and MALDI imaging. When adjacent tissue sections are used, it is, thus, possible to correlate protein identification and molecular imaging. These combined approaches, along with FFPE tissue analysis provide access to massive amounts of archived samples in the clinical pathology setting. Keywords: MALDI • Imaging • FFPE • in situ enzymatic digestion
ISSN:1535-3893
1535-3907
DOI:10.1021/pr060549i