1. A method for quantifying measurements of a protein, the method comprising the steps of: selecting a metric for determining substantially optimal combination of true positives and false positives in at least one data set; applying an optimization technique; and obtaining, from the results of the optimization technique, a value for at least one optimization parameter, said value for at least one optimization parameter resulting in substantially optimal combination of true positives and false positives; wherein the obtaining at least one optimization parameter comprises obtaining a value of a number of independent measures; wherein obtaining a value of a number of independent measures comprises obtaining at least one combination of a value of a number of independent measures and a value for a confidence measure; said independent measures comprising measures of a parameter of the protein obtained using different measurement criteria; wherein a number of true positives and false positives are a function of at least one combination of the number of independent measures and the confidence measure.