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Mini-Complexome Profiling, an FDR-controlled workflow for global targeted Detection of protein complexes (Heart Data)

ABSTRACT: Co-fractionation mass spectrometry experiments (CF-MS) using native-like protein separations such as Blue Native electrophoresis (BNE) or size exclusion chromatography (SEC) enable a global characterization of protein networks, and a better understanding of cellular functions. They do, however, pose significant requirements on sample amounts, on wet lab and on instrument time, which frequently renders statistically useful replication or comparative experiments between multiple biological states non-feasible. Here we present a fast workflow called mini-Complexome Profiling (mCP) for global targeted detection of annotated protein-protein complexes. It comprises mild extraction of complexes, fractionation by BNE and analysis by data independent acquisition mass spectrometry (DIA-MS). Of note, BNE fractionation into 35 fractions is achieved using commercial mini-gels, with minimal requirements on sample amounts. Complexes are detected using a novel, bespoke R package with a controlled false discovery rate (FDR) approach. The tool is available to the community on a Github repository (https://github.com/hugoagno3/mCP ).

INSTRUMENT(S): timsTOF Pro 2

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Heart, Regular Cardiac Myocyte

SUBMITTER: Christof Lenz

LAB HEAD: Christof Lenz

PROVIDER: PXD049426 | Pride | 2024-07-25

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20220414_UP000000589_MUSMU_ref_iRT_Contaminats.fasta	Fasta
	DIANN_VCM_Search.zip	Other
	H_Amedei_07112022_P33_1254_WT_LV_A_01_RA1_1_6749.d.zip	Other
	H_Amedei_07112022_P33_1254_WT_LV_A_02_RA2_1_6750.d.zip	Other
	H_Amedei_07112022_P33_1254_WT_LV_A_03_RA3_1_6751.d.zip	Other

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