Hi,
I set up a combined search in Max quant for the proteomics and phosphoproteomics samples (where I assigned group 1 to proteomics and group 2 to phospho samples). Now when search is finished, how could I differentiate between protein samples and phospho samples, it seems like it does generate phospho (STY) file but where does the protein results go? If I see protein groups file, i think it contains both protein and phospho.
Even though you have defined different group specific parameters, you have still analyzed all samples in one session. Consequently, all results will be in the same output file. To differentiate, use e.g. Perseus to filter the data.
Is there any other way except perseus which i can use to differenriate the group specific data ?
Although less elegant, you would also be able to do it excel or R or something similar. The main issue is that because you analyzed in one run, both base peptides and phosphor-enriched peptides will be annotated to the same proteins, and as such, you cannot distinguish directly. You could filter out all-zero proteins for one condition, but it depends on what you want to do with the data. If you really need to look at them separately, I would suggest running them again in two runs.
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