I have received data that reports on a pull-down experiment. The protein concentrations in different samples is not the same and so I want to know how much of the pulled-down protein is in one sample, relative to the others. I.e. I don't really want to know the exaxt amount of protein, only whether sample 1 contains perhaps 2 times as much protein as in sample 2, so that I can scale the rest of the results.
If sample 1 shows that of the exact same protein the total number of identified peptides is twice that as in sample 2, shouldn't the LFQ/iBAQ values show roughly a twice strong intensity value?
@Jasper, LFQ and iBAQ are two different quantitative approaches, which are good for between sample and in-sample analysis, respectively.
LFQ assumes that the conditions between samples are fairly constant and that concentrations of the majority of proteins hence are the same. It then calculates weights for normalization based on that assumption in order to evaluate e.g. up- and down-regulation between e.g different treatments. Yours being pull down data, this will probably not apply as conditions are likely not comparable after pull down (unless all datasets are from the same pull down method, in which case it may give an estimate).
iBAQ uses the theoretical number of tryptic peptides to normalize each protein within the same sample. That means that by normalizing by the sum of all iBAQs (after removing contaminants and reverse hits), you can estimate the relative molar distribution of proteins within a sample.
But since you have only pull down data and because conditions may not be able to regard as comparable (as you cannot normalize for pull down efficiency etc) it may be difficult to do quantitative comparison as you describe without spiked in quantitative standard protein(s).
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