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Combination of digital microfluidics and magnetic bead-based intact proteoform elution for top-down nanoproteomics of single C. elegans

ABSTRACT: While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up LC-MS workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we here established a facile one-pot sample preparation protocol based on protein aggregation on magnetic beads and intact proteoform elution using 40% v/v formic acid. Performed on a digital microfluidics device, the workflow enabled sensitive analysis of single Caenorhabditis elegans nematodes, increasing the number of proteoform identifications compared to in-tube sample preparation by 46%. Label-free quantification of single nematodes grown under different conditions allowed to identify changes in abundance of proteoforms not distinguishable by bottom-up proteomics. The workflow presented here will help to elucidate cellular changes on the proteoform level in other samples of limited availability.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Whole Body

SUBMITTER: Andreas Tholey

LAB HEAD: Andreas Tholey

PROVIDER: PXD039883 | Pride | 2023-06-19

REPOSITORIES: Pride

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			Action	DRS
	030322_BS_single_worm_TD-SP3-40-FA_SDS_C4_4CVs_15ul_180min_R2.pdResult	Other
	030322_BS_single_worm_TD-SP3-40-FA_SDS_C4_4CVs_15ul_180min_R2.raw	Raw
	030322_BS_single_worm_TD-SP3-40-FA_SDS_C4_4CVs_15ul_180min_R4.pdResult	Other
	030322_BS_single_worm_TD-SP3-40-FA_SDS_C4_4CVs_15ul_180min_R4.raw	Raw
	030322_BS_single_worm_TD-SP3-40-FA_SDS_C4_4CVs_15ul_180min_R5.pdResult	Other

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