Dataset Information

A rapid workflow for high-throughput FFPE-based quantitative proteomics

ABSTRACT: Formalin-fixed, paraffin-embedded (FFPE) tissue samples are an invaluable resource to study the underlying molecular mechanisms of the diseases and when coupled with laser capture microdissection (LCM, isolation of sub histological regions of the tissue sections is readily obtained for further analysis. LCM-based FFPE tissue proteomics is gaining clinicopathological significance particularly in biomarker discovery driven research, beyond its conventional morphology-based application in laboratory diagnosis. Processing of laser capture microdissected tissue sections can be challenging for quantitative proteomic analysis due to lower amount of protein retrieved and losses during the sample processing. A robust, streamlined and automated sample preparation workflow for efficient processing of large cohort of LCM samples which is a primary requisite for biomarker type of studies is needed. Here, we propose a new sample processing workflow for processing of FFPE samples and enable scalable, automated extraction of clean peptides from unprocessed or H&E-stained FFPE tissue sections for deep bottom-up protein profiling and quantification.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

SUBMITTER: Benjamin Madden

LAB HEAD: Akhilesh Pandey

PROVIDER: PXD040727 | Pride | 2023-10-24

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	CE1_2023Feb10_Covaris_A01.mgf	Mgf
	CE1_2023Feb10_Covaris_A01.raw	Raw
	CE1_2023Feb10_Covaris_A02.mgf	Mgf
	CE1_2023Feb10_Covaris_A02.raw	Raw
	CE1_2023Feb10_Covaris_A03.mgf	Mgf

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Publications

A High-Throughput Workflow for FFPE Tissue Proteomics.

Pujari Ganesh P GP Mangalaparthi Kiran K KK Madden Benjamin J BJ Bhat Firdous A FA Charlesworth M Cristine MC French Amy J AJ Sachdeva Gunveen G Daviso Eugenio E Thomann Ulrich U McCarthy Patrick P Vasantgadkar Sameer S Bhattacharyya Debadeep D Pandey Akhilesh A

Journal of the American Society for Mass Spectrometry 20230602 7

Laser capture microdissection (LCM) has become an indispensable tool for mass spectrometry-based proteomic analysis of specific regions obtained from formalin-fixed paraffin-embedded (FFPE) tissue samples in both clinical and research settings. Low protein yields from LCM samples along with laborious sample processing steps present challenges for proteomic analysis without sacrificing protein and peptide recovery. Automation of sample preparation workflows is still under development, especially ...[more]

PMID: 37267530

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