A protocol for the acquisition of comprehensive proteomics data from single cases using formalin-fixed paraffin embedded sections
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Date
2022
Authors
Acland, M.
Mittal, P.
Arentz, G.
Whitehead, F.
Hoffmann, P.
Klingler Hoffmann, M.
Oehler, M.K.
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Journal article
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Methods and Protocols, 2022; 5(4, article no. 57):1-17
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Abstract
The molecular analysis of small or rare patient tissue samples is challenging and often limited by available technologies and resources, such as reliable antibodies against a protein of interest. Although targeted approaches provide some insight, here, we describe the workflow of two complementary mass spectrometry approaches, which provide a more comprehensive and non-biased analysis of the molecular features of the tissue of interest. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) generates spatial intensity maps of molecular features, which can be easily correlated with histology. Additionally, liquid chromatography tandem mass spectrometry (LC-MS/MS) can identify and quantify proteins of interest from a consecutive section of the same tissue.
Here, we present data from concurrent precancerous lesions from the endometrium and fallopian tube of a single patient. Using this complementary approach, we monitored the abundance of hundreds of proteins within the precancerous and neighboring healthy regions. The method described here represents a useful tool to maximize the number of molecular data acquired from small sample sizes or even from a single case. Our initial data are indicative of a migratory phenotype in these lesions and warrant further research into their malignant capabilities.
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Data source: Supplementary materials, https://www.mdpi.com/article/10.3390/mps5040057/s1
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Copyright 2022 by the authors. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license. (https://creativecommons.org/licenses/by/4.0/)