Hi, I have two different groups - control and diseased, with 4 biological replicates in each. I labelled tryptic peptides from each with iTRAQ 8-plex, so 4 per group. Now I am trying to analyse the data on Mascot but it will only give me ratios that compare to the 113 reporter. Should I have pooled all of the control samples and labelled them with 113?
Stephan Jung
Hi,
log into your Mascot server (Home) into the configuration Editor.
There you select the Option Quantitation.
Select the Quantitation Methods iTRAQ 8plex and change in the settings the Denominator to your corresponding control groups. Actually, you need to change this for each of your iTRAQ channel.
I do hope this will help you!
Cheers
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