Abstract: A method of liquid chromatographic retention time-dependent intelligent selected reaction monitoring mass spectrometry (iSRM MS) was established for the identification of targeted proteome, and was compared in detail with the method without liquid chromatographic retention time-dependent iSRM MS in the analysis results of different samples, such as the peptide mixtures from bovine serum albumin, six standard proteins or Thermoanaerobacter tengcongensis extract digested by trypsin. The results showed that the throughput of the identified peptides and the proteins was evidently increased with the method of liquid chromatographic retention time-dependent iSRM MS, especially in the complex sample such as Thermoanaerobacter tengcongensis extract. The coverage of the identified peptides and proteins from Thermoanaerobacter tengcongensis extract was reached 89.62% and 92.41% of the number of targeted peptides and proteins respectively. Higher sensitivity and reproducibility were also obtained. In addition, peptides with the same m/z but different retention times could be identified accurately when the method was used. With the higher throughput, better sensitivity and excellent reproducibility, the method of liquid chromatographic retention time-dependent iSRM MS can play an important role in the identification of targeted proteomes of complex biological samples in the future.

Key words: intelligent selected reaction monitoring (iSRM), mass spectrometry (MS), retention time, targeted proteomics, Thermoanaerobacter tengcongensis, liquid chromatography (LC)