This is part of the online course Experimental Design and Data-Analysis in Label-Free Quantitative LC/MS Proteomics - A Tutorial with msqrob2 (hupo21)
Additional resources
Heart example
Figure 3. Heart
Researchers have assessed the proteome in different regions of the heart for 3 patients (identifiers 3, 4, and 8). For each patient they sampled the left atrium (LA), right atrium (RA), left ventricle (LV) and the right ventricle (RV). The data are a small subset of the public dataset PXD006675 on PRIDE.
Suppose that researchers are mainly interested in comparing the ventricular to the atrial proteome. Particularly, they would like to compare the expression between - the left atrium to the left ventricle - the right atrium to the right ventricle - the average ventricular vs atrial proteome and - if ventricular vs atrial proteome shifts differ between left and right heart region.