Microwave power is a key factor for ion fragmentation. The effect of microwave power on the signal intensities of main ions of analyte was investigated by using MPTDI-TOF MS. By raising the microwave power in increments of 10 watt from 30 to 150 watt, the protonated molecular ions with little fragmentation ions were mainly observed at low microwave power (≤40 W), as shown in the representative graph of theophylline (Figure 4a). The greatest signal intensities of the protonated species were observed when the microwave power reached to 50–70 watt for all 10 tablets. The highest signal intensity of protonated theophylline (m/z 181) with low signal intensity fragmentation ions (m/z 124, 96) were observed when the microwave power was at 70 watt (Figure 4a). In Figure 4b, the highest intensity of protonated metronidazole molecular ion at m/z 172 with its major fragment ions at m/z 128 and m/z 98 were observed at 60 watt. Higher microwave power (>60 watt) would induce MEISD and lead to high abundance of fragmentation ions, which corresponded to the MSn (n =2, 3) fragmentation ions detected by MPTDI-LTQ MS in selective ion mode, indicating a valid MEISD. The fragmentation pathways that occurred in ion source of MPTDI-TOF MS were verified by tandem and multi-stage MPT-LTQ mass spectra of analytes (Supplementary Figure S-1c, j). The MS2 ion at m/z 124 was formed from the fragmentation of parent ion at m/z 181; the MS3 ion at m/z 96 was produced from the MS2 ion at m/z 124 by MPTDI-LTQ MS in selected ion mode. The MS2 ion at m/z 128 was produced from the fragmentation of parent ion at m/z 172; the MS3 ion at m/z 98 was formed from the MS2 ion at m/z 128.Figure 4Influence of the microwave power of MPT ion source on signal intensities obtained for theophylline (a) and metronidazole, (b) in positive mode. *b1 is the signal intensity versus microwave curves for ions of metronidazole at m/z 172, 128, 98; b2 is the enlarged figure for ions at m/z 99 and 128. Instrument: MPT-TOF mass spectrometer