Finding Differential Phosphosites in TMT Phosphoproteomics Data

Question

[jesswhitts]

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

[ATpoint]

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.