Finding Differential Phosphosites in TMT Phosphoproteomics Data
Hello,
Can anyone recommend bioinformatics tools for finding differential phosphosites between conditions, in phosphoproteomics data?
For proteomics, I use DEqMS, is this fine to use for this purpose also?
I looked at using PhosR, but struggling with the batch correction steps (I'm using a cell line for which this is the first phospho dataset we've generated, so can't generate SPSs, and there are batch effects in my data)
Many thanks! Jess
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I am not too deep into MS, but for differential analysis, isn't it always a matrix with rows being peptides/sites/proteins and columns being samples? On log2 scale? If so, use DEqMS or limma directly.