I'm analyzing recombination protein samples that contain a lot of predictable PTMs. Using MaxQuant output tables: From either the ProteinGroups table or Petides table I can obtain the intensity values for a specific protein or peptide respectively. Do these intensity values include peptides that contain a modification?
I would have assumed they would have included all peptides (modified + unmodified); however, in my most recent experiment, there were samples where the intensity of a particular modification (intensity values obtained from the modification sites tables) was greater than the total modification intensity for that protein as obtained from the ProteinGroups table? Can anyone explain this?
Dear Travis,
MQ is only involving peptides with modifications for Oxidation (M) and Acetylation (Protein N-term) by default. You can change this default settings in MQ in "Global Parameters" in the tab "Protein quantification" at "Use only unmodified peptides and …" by selection of your PTM of your interest. I hope this info can help with your question.
Best,
Murat
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