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Questions tagged [peptide-shaker]

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How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
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plot the relation between RMSD and free energy

how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation
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