I performed MS/MS on urinary exosomes from two sets of patients, in order to determine differential expression. However, we found that intensity values vary greatly between samples, given that the number of vesicles vary depending on how concentrated urine is. Could we use another parameter like urinary creatinine to somehow normalize this intensity values?
Hi Eric Raul Barros
Yes, you can use iBAQ values in case your data is label-free. Then you can do sum normalization of the entire matrix followed by log(x) transformation of your data. This will give you distributed iBAQ which can be used for getting differential expression of your data.
In case your are using Proteome Discoverer 2.2, you can use MINORA feature detection in the processing node which will give you intensity which can be used to do sum normalization of the entire matrix followed by log(x) transformation.
Hope this helps!
Varsha
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