how to compare proteomics data?

Question

[siinemselvi]

I have proteome data for control and disease. I should compare their proteins for what differences between them. which tools you recommed? Thank you

Answer 1

[Benn]

If your data is properly normalized, you can try limma. I have been using limma for LFQ normalized ms/ms data. Of course you need biological replicates (if you have them it is not clear from your post).

[Kevin Blighe]

As per b.nota, limma is quite valid (I have also used it) - just ensure that your data distribution is normal. Others just use standard statistical tests, like t-test, ANOVA, etc. If your data distribution is not normal (or you have low sample n), then ensure that you use a non-parametric test (Mann-Whitney test, Kruskal-Wallis ANOVA, et cetera).