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Electrophoresis-Correlative Data-Independent Acquisition (Eco-DIA) Improves the Sensitivity of Mass Spectrometry for Limited Proteome Amounts

ABSTRACT: In this project, we developed electrophoresis-correlative (Eco) data-independent acquisition (DIA) mass spectrometry (MS). We recognized a correlation between the measured mass-to-charge (m/z) and migration time (MT) for peptides during capillary electrophoresis (CE) electrospray ionization (ESI) MS. We leveraged this relationship to dynamically tailor the experimental settings of DIA on an orbitrap mass spectrometer. This approach substantially improved utilization of the limited duty cycle during tandem MS and detection sensitivity compared to the classical DIA. From 1 ng of the standard HeLa proteome digest, Eco-DIA identified ~38% more proteins than conventional DIA, without the assistance of a project-specific spectral library. Proteins that were quantified exclusively by Eco-DIA were in the lower abundance range. Eco-DIA improved the sensitivity of detection from limited amounts of proteomes using CE-ESI-MS.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Peter Nemes

LAB HEAD: Peter Nemes

PROVIDER: PXD051717 | Pride | 2024-09-17

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	2021_HeLa_uniprotFASTA.fasta	Fasta
	2022_10_08_BS03_HeLa_1ng_DIA.RAW	Raw
	2022_10_08_BS03_HeLa_1ng_DIA_librarybased.sne	Other
	2022_10_08_BS03_HeLa_1ng_DIA_libraryfree_rep1.sne	Other
	2022_10_08_BS04_HeLa_1ng_EcoMS.RAW	Raw

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