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  PROMISed: A novel web-based tool to facilitate analysis and visualization of the molecular interaction networks from co-fractionation mass spectrometry (CF-MS) experiments

Schlossarek, D., Luzarowski, M., Sokolowska, E., Gorka, M., Willmitzer, L., & Skirycz, A. (2021). PROMISed: A novel web-based tool to facilitate analysis and visualization of the molecular interaction networks from co-fractionation mass spectrometry (CF-MS) experiments. Computational and Structural Biotechnology Journal. doi:10.1016/j.csbj.2021.08.042.

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 Creators:
Schlossarek, D.1, Author              
Luzarowski, M.2, Author              
Sokolowska, E.1, Author              
Gorka, M.1, Author              
Willmitzer, L.2, Author              
Skirycz, A.1, Author              
Affiliations:
1Small-Molecule Signalling, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_2586692              
2Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              

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Free keywords: Co-fractionation mass spectrometry, CF-MS, Protein-protein complexes, proteinmetabolite complexes, User-friendly app
 Abstract: Co-fractionation mass spectrometry (CF-MS)-based approaches enable cell-wide identification of protein-protein and protein-metabolite complexes present in the cellular lysate. CF-MS combines biochemical separation of molecular complexes with an untargeted mass-spectrometry-based proteomics and/or metabolomics analysis of the obtained fractions, and is used to delineate putative interactors. CF-MS data are a treasure trove for biological discovery. To facilitate analysis and visualization of original or publically available CF-MS datasets, we designed PROMISed, a user-friendly tool available online via https://myshiny.mpimp-golm.mpg.de/PDP1/ or as a repository via https://github.com/DennisSchlossarek/PROMISed. Specifically, starting with raw fractionation profiles, PROMISed (i) contains activities for data pre-processing and normalization, (ii) deconvolutes complex fractionation profiles into single, distinct peaks, (iii) identifies co-eluting protein–protein or protein–metabolite pairs using user-defined correlation methods, and (iv) performs co-fractionation network analysis. Given multiple CF-MS datasets, for instance representing different environmental condition, PROMISed allows to select for proteins and metabolites that differ in their elution profile, which may indicate change in the interaction status. But it also enables the identification of protein–protein and protein–metabolite pairs that co-elute together across multiple datasets. PROMISed enables users to (i) easily adjust parameters at each step of the analysis, (ii) download partial and final results, and (iii) select among different data-visualization options. PROMISed renders CF-MS data accessible to a broad scientific audience, allowing users with no computational or statistical background to look for novel protein–protein and protein–metabolite complexes for further experimental validation.

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Language(s): eng - English
 Dates: 2021
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1016/j.csbj.2021.08.042
 Degree: -

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Title: Computational and Structural Biotechnology Journal
Source Genre: Journal
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Publ. Info: Amsterdam : Elsevier
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 2001-0370
CoNE: https://pure.mpg.de/cone/journals/resource/2001-0370