Dear Skyline team,
Regarding the summation of intensities to determine protein and peptide values for statistical testing with Skyline:
If I compare two or more conditions at the protein level and I have several peptides per protein that all reflect the difference, although are at different intensities, can this be used to influence the statistical significance of the summed protein intensity, i.e. on account of having three measures, or is the information lost by summation (particularly when the base intensities of the different peptides differ by an order of magnitude)?
Thanks in advance,