MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications

Martín-Campos, Trinidad; Mylonas, Roman; Masselot, Alexandre; Waridel, Patrice; Petricevic, Tanja; Xénarios, Ioannis; Quadroni, Manfredo

doi:10.1021/acs.jproteome.7b00194

Cited by 10 publications

(7 citation statements)

References 23 publications

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“…MsViz software (Martín-Campos et al, 2017) was used to compare sequence coverage and phosphorylation of the AMPK alpha 2 protein in the in vitro experiments.…”

Section: Mass Spectrometrymentioning

confidence: 99%

CDK4 Phosphorylates AMPKα2 to Inhibit Its Activity and Repress Fatty Acid Oxidation

et al. 2017

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The roles of CDK4 in the cell cycle have been extensively studied, but less is known about the mechanisms underlying the metabolic regulation by CDK4. Here, we report that CDK4 promotes anaerobic glycolysis and represses fatty acid oxidation in mouse embryonic fibroblasts (MEFs) by targeting the AMP-activated protein kinase (AMPK). We also show that fatty acid oxidation (FAO) is specifically induced by AMPK complexes containing the α2 subunit. Moreover, we report that CDK4 represses FAO through direct phosphorylation and inhibition of AMPKα2. The expression of non-phosphorylatable AMPKα2 mutants, or the use of a CDK4 inhibitor, increased FAO rates in MEFs and myotubes. In addition, Cdk4 mice have increased oxidative metabolism and exercise capacity. Inhibition of CDK4 mimicked these alterations in normal mice, but not when skeletal muscle was AMPK deficient. This novel mechanism explains how CDK4 promotes anabolism by blocking catabolic processes (FAO) that are activated by AMPK.

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“…MsViz software (Martín-Campos et al, 2017) was used to compare sequence coverage and phosphorylation of the AMPK alpha 2 protein in the in vitro experiments.…”

Section: Mass Spectrometrymentioning

confidence: 99%

CDK4 Phosphorylates AMPKα2 to Inhibit Its Activity and Repress Fatty Acid Oxidation

et al. 2017

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“…Proteins sharing significant peptide evidence were grouped into clusters. MsViz 47 software was used to compare sequence coverage and phosphorylation of the PKS4 protein between the dark and light treatments. We obtained a coverage of 59 and 54% of the dark- and light-treated samples respectively.…”

Section: Methodsmentioning

confidence: 99%

A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process

et al. 2018

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Phototropins are light-activated protein kinases, which contribute to photosynthesis optimization both through enhancement of photon absorption when light is limiting and avoidance responses in high light. This duality is in part endowed by the presence of phototropins with different photosensitivity (phot1 and phot2). Here we show that phot1, which senses low light to promote positive phototropism (growth towards the light), also limits the response in high light. This response depends in part on phot1-mediated phosphorylation of Phytochrome Kinase Substrate 4 (PKS4). This light-regulated phosphorylation switch changes PKS4 from a phototropism enhancer in low light to a factor limiting the process in high light. In such conditions phot1 and PKS4 phosphorylation prevent phototropic responses to shallow light gradients and limit phototropism in a natural high light environment. Hence, by modifying PKS4 activity in high light the phot1-PKS4 regulon enables appropriate physiological adaptations over a range of light intensities.

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“…Many of the existing PTM analysis tools offer great data visualisation features. For example, Cytoscape with its many visualization apps including PTMOracle and STRING for PPI and networks; Protein data bank and PTM-SD for protein structures [158]; ProHits-viz [159], a suite of web tools for visualizing interaction proteomics data; MsViz [160], a graphical tool for manual validation and quantification of PTMs for small to medium scale experiments.…”

Section: Online Tools For Subsequent Analysismentioning

confidence: 99%

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools

Pascovici

McKay

et al. 2018

IJMS

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Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra—many of which likely harbour PTMs—through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.

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MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications

Cited by 10 publications

References 23 publications

CDK4 Phosphorylates AMPKα2 to Inhibit Its Activity and Repress Fatty Acid Oxidation

CDK4 Phosphorylates AMPKα2 to Inhibit Its Activity and Repress Fatty Acid Oxidation

A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools

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