Perseus-PHOTON exsample data

[wanghao1991217]

Hi, I'm just starting to learn to using the PHOTON. I download the phosphoSTY_rudolph.txt and load it into Perseus and follow the Data preparation wokflow.

what is the data type of the first four columns of this data? Are the first two columns the fold changes of EGF related experimental group relative to the control group? If so, how does the fold changes to be calculated? Is the quantitative value of each experimental group divided by the average value of the control group？

Thank you for your contribution and hope to answer my confusion.

[jdrudolph]

You can check out the raw data and experiment description in the original paper. https://www.cell.com/fulltext/S2405-4712(16)30369-6 I hope this clears things up.
In short: the listed values are SILAC ratios from single experiments.

[wanghao1991217]

You can check out the raw data and experiment description in the original paper. https://www.cell.com/fulltext/S2405-4712(16)30369-6 I hope this clears things up.
In short: the listed values are SILAC ratios from single experiments.

Thank you. My own data were lable free quantification phosphoproteomics with two groups, each with three biological replicates. Should I use the Log2 fold change as input data when using photo , in addition, should the fold change need to be filtered by the p value (for exsample : p < 0.05) ?