Fig. 3.

Multiplex assay development. A, representative scheduled LC-MS/MS assay monitoring multiple reporter peptides corresponding to transcription factors regulating embryonic stem cell fate. Four exogenous sentinel marker peptides are jointly monitored in parallel to calculate relative retention time (stored in relational database) to control target data acquisition windows (gray highlights). The XIC of the most intense product ions of each peptide is indicated. B, heat map showing ion abundances for peptide standard curves generated using synthetic peptides alone or after spiking of the reference standards into a digested mESC NE. The zoom-ins show selectively linear signal response over 3 orders of magnitude (10-fold dilutions from 1 pmol to 1 fmol) using log-log (base 10) plots.