The results of our study show that peptide intensity based quantification methods perform favorably in terms of mean fold error of protein amount estimates, when compared to spectral count based quantification methods. In the choice between different flavors of peptide intensity based quantification methods we favor the "Best-flyer method" over peptide intensity sum methods, as the Top3 method display better linear characteristics with respect to protein amount, throughout the full concentration range. Unless using a different regression model than the typically employed power regression, peptide intensity sum methods, tend to introduce biased protein amount estimation errors.
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