1. A method comprising: in a computer, computing a reproducibility score based on a peak association matrix and a mass/charge association map to test whether an isotope cluster, a label set, or a charge group is reproducible, wherein the computing of the reproducibility score comprises generating a three-dimensional array from the peak association matrix and the mass/charge association map, averaging rows of the peak association matrix to generate a first matrix of average vectors, calculating a first matrix of assimilated vectors from intensity values of the peak association matrix, and computing a first correlation coefficient using at least the first matrix of average vectors and the first matrix of assimilated vectors; and computing a quality score by scoring a transposed peak association matrix together with the mass/charge association map to test whether the isotope cluster, the label set, or the charge group is well formed, wherein the computing of the quality score comprises transposing the peak association matrix to generate the transposed peak association matrix, averaging rows of the transposed peak association matrix to generate a second matrix of average vectors, calculating a second matrix of assimilated vectors from the transposed peak association matrix, and computing a second correlation coefficient using at least the second matrix of average vectors and the second matrix of assimilated vectors.