Efficient Method for the Proteomic Analysis of Fixed and Embedded Tissues

Palmer-Toy, Darryl E.; Krastins, Bryan; Sarracino, David; Nadol, Joseph B.; Merchant, Saumil N.

doi:10.1021/pr050208p

Cited by 130 publications

(144 citation statements)

References 8 publications

(9 reference statements)

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“…A total of 12 855 fully tryptic peptides are identified from the FFPE tissue section treated with the heat-induced AR approach, leading to the identification of 3263 distinct proteins. By comparison with the reported FFPE tissue-based proteome studies [45,71,72], our results present the most comprehensive analysis of human tissue proteomics including the identification of low-abundance membrane proteins (Fig. 8).…”

Section: Formalin-fixed and Paraffin-embedded Tissuesmentioning

confidence: 75%

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Capillary separations enabling tissue proteomics‐based biomarker discovery

et al. 2006

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Development of the capability to enable large‐scale proteome studies, analogous to comprehensive gene expression analysis, will clearly have far‐reaching impacts on protein biomarker investigations of human diseases such as cancer through interrogation of the archived fresh frozen and formalin‐fixed and paraffin‐embedded tissue collections. This review therefore focuses on the most recent advances in microdissection techniques and proteome platforms for procuring homogeneous subpopulations of tumor cells or structures and performing comprehensive analysis of protein profiles within tissue specimens, respectively. Developments in capillary separations capable of providing extremely high resolving power and selective analyte enrichment are particularly highlighted for their roles within the broader context of a state‐of‐the‐art integrated tissue proteome effort. The capabilities of CIEF‐based multidimensional separations for performing proteome analysis from minute samples create new opportunities in the pursuit of biomarker discovery using enriched and selected cell populations procured from tissue specimens. These proteome technological advances combined with recently developed tissue microdissection techniques provide powerful tools for those seeking to gain a greater understanding at the global level of the cellular machinery associated with human diseases such as cancer.

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Section: Formalin-fixed and Paraffin-embedded Tissuesmentioning

confidence: 75%

“…8). Again, the application of only single-dimension chromatography separation in these recent studies [45,71,72] has significantly limited the dynamic range and detection sensitivity of MS measurements and greatly impacted their ability to mine deeper into the tissue proteome.…”

Section: Formalin-fixed and Paraffin-embedded Tissuesmentioning

confidence: 99%

Capillary separations enabling tissue proteomics‐based biomarker discovery

et al. 2006

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“…Indeed, the main concern about the use of these FFPE tissues is to apply a procedure that could give rise to the largest molecular information, compared to the one available using fr/fr tissues. Generally, fr/fr tissues give a higher number of proteins compared to FFPE tissues (Giusti and Lucacchini, 2013), but some studies reported a better proteins identifications recovery with FFPE tissues (Nirmalan et al, 2011;Palmer-Toy et al, 2005;Shi et al, 2006). These comparisons highlight the importance of the chemical treatments for efficient FFPE tissue preparation.…”

Section: Optimal Tissue Solubilization Towards Protein Extractionmentioning

confidence: 97%

Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology

Longuespée

Fléron

Pottier

et al. 2014

OMICS: A Journal of Integrative Biology

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“…Apart from its traditional use in histological evaluation and research in immunohistochemistry (IHC) for previously known proteins (Ramos-Vara 2005), the potential of FFPE tissue collections as an alternative to fresh-frozen tissues for biomarker discovery has come into realization (Hood et al 2006;Nirmalan et al 2008). Efforts and achievements have been made in unlocking proteins from formaldehyde-induced extensive protein/DNA/RNA crosslinking and in mining the FFPE tissue proteome by mass spectrometry (MS) (Ikeda et al 1998;Crockett et al 2005;Palmer-Toy et al 2005;Shi et al 2006;Fowler et al 2007Fowler et al ,2008Ronci et al 2008;Xu et al 2008). Additionally, comparisons of proteomic analysis of paired frozen and FFPE tissue specimens were reported (Hood et al 2005;Guo et al 2007).…”

Section: Abstract Npc Ffpe Itraq 2d Lc-ms/msmentioning

confidence: 99%

Quantitative Proteomic Analysis of Formalin-fixed and Paraffin-embedded Nasopharyngeal Carcinoma Using iTRAQ Labeling, Two-dimensional Liquid Chromatography, and Tandem Mass Spectrometry

Xiao

Chen

et al. 2010

J Histochem Cytochem.

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S U M M A R Y Formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a potentially valuable resource for protein biomarker investigations. In this study, proteins were extracted by a heat-induced antigen retrieval technique combined with a retrieval solution containing 2% SDS from FFPE tissues of normal nasopharyngeal epithelial tissues (NNET) and three histological types of nasopharyngeal carcinoma (NPC) with diverse differentiation degrees. Then two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling was employed to quantitatively identify the differentially expressed proteins among the types of NPC FFPE tissues. Our study resulted in the identification of 730 unique proteins, the distributions of subcellular localizations and molecular functions of which were similar to those of the proteomic database of human NPC and NNET that we had set up based on the frozen tissues. Additionally, the relative expression levels of cathepsin D, keratin8, SFN, and stathmin1 identified and quantified in this report were consistent with the immunohistochemistry results acquired in our previous study. In conclusion, we have developed an effective approach to identifying protein changes in FFPE NPC tissues utilizing iTRAQ technology in conjunction with an economical and easily accessible sample preparation method. (J Histochem Cytochem 58:517-527, 2010)

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Efficient Method for the Proteomic Analysis of Fixed and Embedded Tissues

Cited by 130 publications

References 8 publications

Capillary separations enabling tissue proteomics‐based biomarker discovery

Capillary separations enabling tissue proteomics‐based biomarker discovery

Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology

Quantitative Proteomic Analysis of Formalin-fixed and Paraffin-embedded Nasopharyngeal Carcinoma Using iTRAQ Labeling, Two-dimensional Liquid Chromatography, and Tandem Mass Spectrometry

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