We present the simple approach for the combination of different ion sources on a single mass spectrometer without any interference between them. Each ion source can be positioned as far as 1 m from the mass spectrometer; ions are transported by the means of flexible copper tubes, which are connected, to the separate inlet capillaries. Special valves enable switching channels on and off. Using this approach, we successfully combined native electrospray ionization (ESI), regular ESI, β-electrons ionization, and atmospheric pressure photoionization (APPI) of thermally desorbed vapors of petroleum on a single mass spectrometer. In addition, separate channels allow infusing internal calibration mixture or performing ion molecular reactions in one channel and using the other as a reference. Using this idea, we have developed an original sequential window acquisition of all theoretical mass spectra (SWATH MS) approach in which peptide ions are transported in different channels, one of which is heated to high temperature so that ions are thermally fragmented, and the other channel ensures the presence of nonfragmented ions in the spectrum. Also, we demonstrated the possibility to perform gas phase H/D exchange reaction in one channel and using another as reference. Use of valves makes it possible to exclude any interference between them. Thus, we have demonstrated the possibility to create a multichannel system in which ions would be transported through several inlet tubes in which different ion molecular reactions such as Paternò-Büchi, ozonation, or H/D exchange will occur. Comparison of mass spectra recorded when different channels are open will provide structural and chemical information about unknown species.