Fig. 4.

Peptide identification and quantification using TCorr. A, representative correlograms showing the chromatographic profile of TCorr scores (0. 95 and higher) calculated for experimental MS/MS spectra recorded for spiked synthetic (left) or endogenous (right) Pou5f1 peptide FEALQLSLK in mESC NE matched against the corresponding reference spectral library over a specified retention time window 66- 86 min. Significant similarity in the observed b- and y-product ion intensity patterns occurs regardless of background interferences, allowing the XIC of the most intense target precursor-to-product ion transition to be reliably quantified. The gray highlights correspond to high confidence matches represented by the highest consecutive TCorr correlation scores. B, comparison of exemplar MS/MS spectra obtained for spiked and endogenous peptide (top) versus the corresponding library reference (bottom). XCorr correlation scores of a SEQUEST database search are indicated and obtained for the correct sequence FEALQLSLK. C, representative relative peak intensities of all b/y-ion transitions (TCorr-FULL) and TCorr-correlation score of 0.963 are shown. D, improved TCorr score 0.987 for endogenous peptide based on selected transitions freed from potential interferences (TCorr-TRANSITION).