in mass spectrometry the "peptide match score summation" (PMSS) is often used as a synthetic quantity to estimate protein abundance. with this parameter you can often compare the levels of the same protein in different samples. what I would like to do instead, is to compare protein abundances within the same samples (analyzed with tandem MS). PMSS is not suitable for this, without normalization steps, because it depends on how a protein gets digested with trypsin and how its peptides get ionized.
I'm not a MS expert, but googling for the answer I could find this paper: http://www.ncbi.nlm.nih.gov/pubmed/18772871, which tries to correct for each protein "detectability" and estimate an absolute protein abundance. visiting the tool page, I found out that it was last updated in 2010.
do you know of a more advanced approach to this problem, or a more recent tool?
to be clear, my ultimate goal is to compare protein abundances within the same sample (to say this protein is more abundant than the other)