I hope I am asking to the right place. I am currently analyzing some Mass Spectometry data of 2 mutant phenotypes and the WT with 5 biological replicates each. I have normalized the abundance values of each peptide (and its respective protein) across the samples and now I want to perform a test to identify signifficantly differentially expressed proteins. My thought was to perform standard 2-sample t-tests, comparing the measured abundances for each peptide or protein across the conditions of interest. But being a biologist, I am unsure about the assumptions I am making with these tests and how to perform them using R.
Here is an example of my data:
Normaliz.Abundance_Sample1 Normaliz.Abundance_Sample2 Peptide A 3165565416 757986204 Peptide B 1765535403 2457586199
with the data frame having 15 columns (3x5 experiment) for around 8000 identified proteins.
Really appreciate any kind of help. R.