- I did a Co-IP MS with two samples and got the LFQ data from MaxQuant, and I wanted to normalize it by an internal reference protein. After I divide the LFQ of the other protein by the LFQ of the internal reference protein to get the ratio, how should I calculate the protein expression difference between the two samples?
- Or is this calculation incorrect? And what should I do if I want to normalize with internal reference proteins?
Michal Gorka
Dear Cecilia Liang ,
how many biological replicates do you have ?
I would:
1. Filter data from "only identified by site" and "reverse" hits.
2. Transform value by log2.
3. Potential imputation of missing values
4. Two-sample test.
5. Volcano plot - choose your cutoff
Very simple approach to get some candidates from your CO-IP analysis.
Best,
Michal
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Cecilia Liang
three replicates. And some of the quantitative information in the results belongs to a protein group, how can I know the quantitative information of each protein in that protein group?@ Michal Gorka
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Michal Gorka
Focus on "Major Protein" or "Fasta.Header" column, take LFQ values and follow what I have written in first post. You can also try Perseus software, also developed by Cox Group.
Best,
Michal
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