Proteomics

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Proteomics on formalin-fixed and stained laser-capure microdissected human lung sections


ABSTRACT: A broad range of tissues have been examined by microscopy following a process of formalin fixation, paraffin embedment, sectioning and staining. Haematoxylin and eosin (H&E) – which respectively stain nuclei blue and other cellular and stromal material pink – are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterisation can be achieved by coupling spatially resolved methods to mass spectrometry (MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing, embedding and staining tissues for histological analysis is poorly compatible with standard sample preparation methods for mass spectrometry, resulting in a reduction in the number of proteins identified. Here we describe a microproteomics technique optimised to analyse H&E-stained, formalin-fixed paraffin-embedded (FFPE) sections of human lung tissue. Laser capture microdissection (LCM) was used to isolate sections of morphologically normal alveoli and blood vessels from tissue-banked specimens of human idiopathic pulmonary fibrosis (IPF). Following sample digestion and clean-up, MS was able to identify 1252 differentially expressed proteins. This work provides an optimised pipeline for the analysis of FFPE tissue sections by LCM-MS. Furthermore, it offers proof of principal that MS can identify distinct, characteristic proteomic compositions of anatomical features within complex tissues.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

SUBMITTER: Venkatesh Mallikarjun  

LAB HEAD: Jeremy Herrera

PROVIDER: PXD014762 | Pride | 2021-09-08

REPOSITORIES: Pride

Dataset's files

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Publications

Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues.

Herrera Jeremy A JA   Mallikarjun Venkatesh V   Rosini Silvia S   Montero Maria Angeles MA   Lawless Craig C   Warwood Stacey S   O'Cualain Ronan R   Knight David D   Schwartz Martin A MA   Swift Joe J  

Clinical proteomics 20200617


<h4>Background</h4>Haematoxylin and eosin (H&E)-which respectively stain nuclei blue and other cellular and stromal material pink-are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterization can be achieved by laser capture microdissection coupled to mass spectrometry (LCM-MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing and H&E staining of tissues provides challenges with standard  ...[more]

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