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Vitek-Lab / MSstatsPTM

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments
https://vitek-lab.github.io/MSstatsPTM/
Artistic License 2.0
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LFQ phospho data analysis #88

Closed solabthomas closed 4 months ago

solabthomas commented 4 months ago

Is there any workflow or codes to support LFQ phospho generated from fragpipe. As there is only fragpipe TMT phospho workflow in the examples

tonywu1999 commented 4 months ago

Hi,

For the function FragPipetoMSstatsPTMFormat, you can set the parameter label_type to "LF".

I don't see any examples for LF in the vignettes though. If you have any example datasets from Fragpipe with PTMs, we could add those examples to the vignettes. Otherwise, our team will look to find a dataset ourselves.

solabthomas commented 4 months ago

Hi, thanks for your reply. Yes, I have the generated files and output from LFQ phospho workflow, can I send it to your email account?

Thanks.

tonywu1999 commented 4 months ago

@solabthomas

Yes, you can send it to my northeastern email - ant.wu@northeastern.edu

Thanks, Tony

tonywu1999 commented 4 months ago

Closing in favor of https://github.com/Vitek-Lab/MSstatsPTM/pull/90