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SubCellBarCode: Integrated workflow for robust classification and visualization of spatial proteome

ABSTRACT: We have developed a mass spectrometry (MS) and bioinformatics-based pipeline to generate a proteome-wide resource of protein subcellular localization across multiple human cancer cell lines (www.subcellbarcode.org). Here, we present a detailed wet-lab protocol spanning from subcellular fractionation to MS-sample prep, as well as a dry-lab protocol covering quantitative MS-data analysis, machine-learning-based classification, differential localization analysis and visualization of the output. For broad applicability, we evaluated the pipeline using MS-data generated by three different peptide prefractionation approaches, HiRIEF-LC-MS, High-pH reverse phase fractionation and direct analysis without pre-fractionation using long gradient LC-MS.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Janne Lehtiö

PROVIDER: PXD022533 | JPOST Repository | Mon Sep 26 00:00:00 BST 2022

REPOSITORIES: jPOST

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SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry.

Arslan Taner T Pan Yanbo Y Mermelekas Georgios G Vesterlund Mattias M Orre Lukas M LM Lehtiö Janne J

Nature protocols 20220622 8

The molecular functions of a protein are defined by its inherent properties in relation to its environment and interaction network. Within a cell, this environment and network are defined by the subcellular location of the protein. Consequently, it is crucial to know the localization of a protein to fully understand its functions. Recently, we have developed a mass spectrometry- (MS) and bioinformatics-based pipeline to generate a proteome-wide resource for protein subcellular localization acros ...[more]

PMID: 35732783

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