Analysis of IP-TMT data

[niki...@gmail.com]

Hi there,

I have run an immunoprecipitation experiment of estrogen receptor (my bait) under 3 conditions and each experiment was done 3 times. I have also run next to it an IgG negative control to extract contaminant binding proteins. To be able to quantify this I have then done isobaric labelling using TMT 10-plex. I am wondering if you know how I can normalize an IP to get quantified changes in the binding partners of estrogen receptor under the different conditions. Can I log2 transform and then median-normalize the data at the protein level or it is trickier than whole cell poteome analysis because of the fact that in an IP I cannot assume that most proteins are not changing?

Thank you very much for your help.

Nikiana

[David Bouyssié]

Hi Nikiana,

Could you please merge your question with the previous one (https://groups.google.com/forum/#!topic/proteomicsqa/zswv3H3ucZo)?

We would like to avoid duplicated discussions.

One of my colleagues should answer your questions today.

Best,

David