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Label-free mass spectrometry-based proteomics of lung cancer FFPE glass slides

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 68 FFPE lung cancer biopsies on single glass slides using label-free data-independent acquisition (DIA) MS proteomics. We show data from two instruments, Orbitrap Astral and timsTOF HT. 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: PXD072014 | Pride | 2026-05-26

REPOSITORIES: Pride

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			Action	DRS
	20251103_GMNOOB_FFPE68_DIA_WZ40SPD_sample_W01.raw	Raw
	20251103_GMNOOB_FFPE68_DIA_WZ40SPD_sample_W02.raw	Raw
	20251103_GMNOOB_FFPE68_DIA_WZ40SPD_sample_W03.raw	Raw
	20251103_GMNOOB_FFPE68_DIA_WZ40SPD_sample_W04.raw	Raw
	20251103_GMNOOB_FFPE68_DIA_WZ40SPD_sample_W05.raw	Raw

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