PXD014762-1

PXD014762 is an original dataset announced via ProteomeXchange.

Title	Proteomics on formalin-fixed and stained laser-capure microdissected human lung sections
Description	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.
HostingRepository	PRIDE
AnnounceDate	2021-09-08
AnnouncementXML	Submission_2021-09-08_14:13:17.556.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Venkatesh Mallikarjun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-25 04:15:52	ID requested
⏵ 1	2021-09-08 14:13:18	announced
2	2024-10-22 05:26:45	announced	2024-10-22: Updated project metadata.

Herrera JA, Mallikarjun V, Rosini S, Montero MA, Lawless C, Warwood S, O'Cualain R, Knight D, Schwartz MA, Swift J, Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues. Clin Proteomics, 17():24(2020) [pubmed]

submitter keyword: lung, human, fixed, laser-capture, dissection, spatial proteomics

Jeremy Herrera
contact affiliation	Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
contact email	Jeremy.Herrera@manchester.ac.uk
lab head
Venkatesh Mallikarjun
contact affiliation	University of Manchester
contact email	venkatesh.mallikarjun@manchester.ac.uk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD014762

PRIDE project URI

• PRIDE
  1. PXD014762
     1. Label: PRIDE project
     2. Name: Proteomics on formalin-fixed and stained laser-capure microdissected human lung sections