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Label-free mass spectrometry-based proteomics of lung cancer FFPE scrolls

ABSTRACT: Formalin-fixed, paraffin-embedded (FFPE) is the most common method for preserving tissue material in the clinic with millions of specimens stored in biobanks around the world. However, FFPE samples present challenges for molecular profiling, including proteomics. Nonetheless, optimized sample preparation protocols and next-generation mass spectrometers (MS) enable the analysis of FFPE samples. Here, we analyze 15 FFPE lung cancer specimens, including resected tissue and biopsies using label-free data-independent acquisition (DIA) MS proteomics. We show data from three instruments, including Orbitrap Astral, timsTOF HT, and Orbitrap Exploris. Our analysis shows that label-free proteomics offers rapid, in-depth, reproducible proteome-wide profiling of FFPE tissue samples.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

DISEASE(S): Lung Cancer

SUBMITTER: Georgios Mermelekas

LAB HEAD: Lukas M. Orre

PROVIDER: PXD071948 | Pride | 2026-05-26

REPOSITORIES: Pride

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			Action	DRS
	240731_FFPE-Fenoprep_LungCancer_KS_20min_200ng_DIA_sample01.raw	Raw
	240731_FFPE-Fenoprep_LungCancer_KS_20min_200ng_DIA_sample02.raw	Raw
	240731_FFPE-Fenoprep_LungCancer_KS_20min_200ng_DIA_sample03.raw	Raw
	240731_FFPE-Fenoprep_LungCancer_KS_20min_200ng_DIA_sample04.raw	Raw
	240731_FFPE-Fenoprep_LungCancer_KS_20min_200ng_DIA_sample05.raw	Raw

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