Fig. 3.

PyQuant is capable of increasing the quantification rates of MaxQuant and Proteome Discover. A, PSMs from MaxQuant were extracted and analyzed with PyQuant, which resulted in a 45% increase in the number of spectra quantified as compared with MaxQuant alone. Similarly, PSMs from Proteome Discoverer were analyzed with PyQuant, which resulted in a 25% increase in the number of spectra quantified as compared with Proteome Discover. B, The quantification by PyQuant of a peptide which was not quantified by MaxQuant is shown. The extracted ion chromatogram for each label is robust with multiple isotopomers identified for every label. The quantified ratio as compared with the expected ratio for each channel is shown on the right.