Dataset Information

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):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

SUBMITTER: Venkatesh Mallikarjun