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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 with Reporter. I can load the file with Reporter GUI. Though Reporter is still in development and cannot be run from commandline yet. Are there other tools available that can run from Peptideshaker exported reports for downstream analysis? I tried to run Reporter from commandline version 0.7.16. I will try 0.7.17 which was just released.

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  • $\begingroup$ It seems to me there should be something, but without knowing what you have tried we could repeat the same search you did. What search did you perform? Do you need it to be accessible via command line? $\endgroup$
    – llrs
    Commented Feb 15, 2019 at 8:55

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