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Reproducibility of Protein Identification of Selected Cell Types in Barrett’s Esophagus Analyzed by Combining Laser-Capture Microdissection and Mass Spectrometry

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    Reproducibility of Protein Identification of Selected Cell Types in Barrett’s Esophagus Analyzed by Combining Laser-Capture Microdissection and Mass Spectrometry
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    Erasmus MC, Rotterdam, The Netherlands, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands, and Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
    * To whom correspondence should be addressed. Theo M. Luider, PhD, Department of Neurology, Erasmus Medical Center, P.O. Box 2040 3000 CA Rotterdam, The Netherlands. Tel:+31 10 7038069. Fax: +31 10 7044365. E-mail: [email protected]
    †Erasmus MC.
    ‡Department of Gastroenterology and Hepatology, Academic Medical Center.
    §Department of Pathology, Academic Medical Center.
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2011, 10, 1, 288–298
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    https://doi.org/10.1021/pr100709b
    Published November 5, 2010
    Copyright © 2010 American Chemical Society
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    Abstract

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    Barrett’s esophagus (BE) is associated with increased risk of esophageal adenocarcinoma (EAC) and characterized by replacement of normal esophageal squamous epithelium by columnar epithelium. These alterations are also reflected in changes in the protein-expression profiles of the cell types involved. To separately investigate the proteomes of selected cell-types we combined laser-capture microdissection (LCM) and liquid chromatography−mass spectrometry (LC−MS). Aims were to determine the sensitivity, specificity, and technical reproducibility of the sampling method, and the biological variability within and between biopsies and patients. Frozen biopsies were cryo-sectioned, samples of around 2000 epithelial or stroma cells microdissected, digested and measured by Orbitrap LC−MS. Proteins were then identified by MS/MS database search and quantified by label-free analysis. An average of 366 protein-groups were identified per sample, and more protein-groups were found in epithelial samples than in stromal samples (442 vs 301, p < 0.0001). Altogether, 1254 distinct protein-groups were found, 289 and 88 of them significantly more often in epithelial and stroma samples, respectively. We assessed five different types of reproducibilities (run-to-run, intrabiopsy, biopsy-to-biopsy, experiment-to-experiment, and patient-to-patient) for protein identification and protein quantification. Reproducibility of protein identification ranged from 78 to 57%, and standard deviation of protein quantification was on patient-to-patient level four times higher than for run-to-run. We conclude that sampling around 2000 cells requires groups of 32 samples to detect significant, over 10-fold differences in protein abundances and thus creates a successful compromise between throughput and quality of results. We therefore believe that this method is suitable for investigating protein-expression profiles during carcinogenesis.

    Copyright © 2010 American Chemical Society

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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2011, 10, 1, 288–298
    Click to copy citationCitation copied!
    https://doi.org/10.1021/pr100709b
    Published November 5, 2010
    Copyright © 2010 American Chemical Society
    Request reuse permissions

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