We study the spontaneous emission (SE) of an excited two-level nonrelativistic system (TLS) interacting with the vacuum in a waveguide of rectangular cross section. All TLSs transitions and the center-of-mass motion of the TLS are taken into account. The SE rate and the carried frequency of the emitted photon for the TLS initial being at rest is obtained, it is found in the first order of the center of mass (c.m.) that the frequency of the emitted photon could be smaller or larger than the transition frequency of the TLS but the SE rate is smaller than the SE rate $Gamma_{f}$ of the TLS fixed in the same waveguide. The SE rate and the carried frequency of the emitted photon for the TLS initial being moving is also obtained in the first order of the c.m.. The SE rate is larger than $Gamma_{f}$ but it is independent of the initial momentum. The carried frequency of the emitted photon is creased when it travels along the direction of the initial momentum and is decreased when it travels in the opposite direction of the initial momentum.
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