What are the user friendly R packages available for analyzing shotgun proteomics data?

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5.3 years ago

WUSCHEL ▴ 750

Has anyone had an experience in analyzing shotgun mass spectrometry data (unlabelled) Q-TOF uding R programming?

What are the user-friendly packages with examples?

R proteomics mass spectrometry • 1.4k views

ADD COMMENT • link 5.3 years ago by WUSCHEL ▴ 750

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Please define user-friendly.

ADD REPLY • link 5.3 years ago by Benn 8.3k

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with having access to real-world examples/explanations!

ADD REPLY • link 5.3 years ago by WUSCHEL ▴ 750

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What have your tried? RforProteomics? From where do you want to use R? From RAW data?

ADD REPLY • link 5.3 years ago by Benn 8.3k

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Thanks for trying to help Nota. I have not tried anything yet. Yes from the raw data. (.d files)

ADD REPLY • link 5.3 years ago by WUSCHEL ▴ 750

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I haven't found an R package yet that can start from .RAW files, but there is a linux command line version of MaxQuant available now.

ADD REPLY • link 5.3 years ago by Benn 8.3k

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