I am working on Phosphoproteomics experiment by using SILAC (on S. cerevisiae). I have got back my MS data and was suggested to use Proteome Discoverer 2.2 to analyze the data. Since this is my first time doing Phosphoproteomics, I need to get some advice (and direction) to analyze the data. Does anyone know what is the first thing to look for? (To my understanding, I need to look up the Heavy/Light ratio for the heavy-labelled and light-labelled peptides in order to quantify the protein abundance)
Any inputs are appreciated.
Thank you
Please look at the following below links which may help you in your analysis:
https://www.nature.com/articles/s41467-018-03309-6.pdf
https://sciex.com/Documents/tech%20notes/SWATH-PhosphoProfiling-TN-9460114.pdf
https://www.tandfonline.com/doi/pdf/10.1586/epr.10.104
Thanks
I assume you are using a Thermo MS for your analysis since you are using PD for analysis. In that case, I would strongly recommend you look at using MaxQuant and Perseus for your analysis. Search the literature, there are multiple relevant papers using MQ.
And see here; https://maxquant.org/
Regards,
Peter
Hi Ryan,
Agree with Peters suggestion of Maxquant - there are youtube videos from previous years Maxquant summer schools detailing how to do phospho/PTM analysis with Maxquant and Perseus. I've given links to the PTM-specific videos but the rest of the playlist is also good.
1. https://www.youtube.com/watch?v=7EUmMttFIfo&list=PL6yHRLjecpwB0C0xdEhxiXLV1mXgj4bEO&index=27
2.https://www.youtube.com/watch?v=f5SLpXzc7WM&index=28&list=PL6yHRLjecpwB0C0xdEhxiXLV1mXgj4bEO
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