An example of the development of the SRM descriptor for a target protein.

<p>(A) The identification of glutathione peroxidase 1 (Gpx1) on a capillary column LC-ion trap mass spectrometry system (LTQ-xl, ThermoScientific) in a sample of mouse liver was evaluated to select the best peptides for inclusion in the assay. The chromatographic conditions, including column, solvent program, and flow rate, were comparable to that used on the triple quadrupole system for the final analyses. As a result, a characteristic elution pattern was obtained. (B,C, and D) From the ion trap instrument, full scan collision induced dissociated (CID) spectra were acquired which allows the identification of the respective peptides to be verified. The CID spectra for the peptides (B) FLVGPDGVPVR, (C) NDIAWNFEK, and (D) AHPLFTFLR were obtained. (E) These chromatographic and CID spectra data were used to develop the Gpx1 SRM descriptor that includes parent and product ion <i>m/z</i> to monitor, optimized collision energies for each fragmentation reaction, and a scheduled window for elution. Eventually, only two of the peptides, NDIAWNFEK and AHPLFTFLR were retained in the final assay. A similar approach was used for all other proteins in the antioxidant and stress protein group assay.