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System-wide profiling of protein-complexes via size exclusion chromatography– mass spectrometry (SEC-MS)

ABSTRACT: In living cells most proteins are organized in stable or transient functional assemblies known as protein complexes, which control a multitude of vital cellular processes such as cell cycle progression, metabolism, and signal transduction. System-wide workflows for analysis of protein complexes using mass spectrometry based proteomics consists of a biochemical fractionation methods which take advantage of biophysical features such as charge or mass of protein complexes. In this project, we apply size exclusion chromatography to investigate protein assemblies from a Jurkat whole cell lysate. We introduced a fast and robust in-plate sample preparation workflow which allows for replicates to be performed with fewer technical hurdles and with a high degree of reproducibility) We acquired the data in SWATH-mode in combination with a high-throughput LC-system (EVOSEP one). The bioinformatics pipeline builds on the OpenSWATH workflow combined with CCprofiler, a tool for statistical scoring of protein co-elution profiles. This method enabled us to identify more than 100 protein complexes from mammalian cells within one day of measurement.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Jurkat Cell

SUBMITTER: Fabian Frommelt

LAB HEAD: , Ruedi Aebersold

PROVIDER: PXD018033 | Pride | 2022-05-06

REPOSITORIES: pride

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			Action	DRS
	2020_Methods_in_molecular_biology_information_file.txt	Txt
	HS_decoy_EvosepLib.pqp	Other
	combined_iRT_CiRT_201804.TraML	Other
	feature_alignment.csv	Csv
	vmatej_I190208_001.mzXML.gz	Mzxml

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