Hello everyone. Greetings of the day.
I need help in doing proteomics analysis.
I have MaxQuant output files that contain files : aifMsms.txt, allPeptides.txt, evidence.txt, modificationSpecificPeptides.txt, msms.txt, msmsScans.txt, msScans.txt, mzRange.txt, Oxidation (M)Sites.txt, parameters.txt, peptides.txt, proteinGroups.txt, simPeptides.txt, simScans.txt, summary.txt . I don't understand how to further perform differential expression analysis in R through these files.
I am new to proteomics analysis. So, any help would be appreciated.