Here we present a comparative analysis of vertical minority carrier transport in Si, Si0.925Ge0.075,Si0.998C0.002, and Si0.99C0.01 base layers of bipolar transistors. We show that a conventional transit time analysis for extracting the minority carrier mobilities fails for doping profiles containing a low doped emitter region. The contribution of locally compensated charge storage, called neutral charge storage, in the emitter-base depletion region must not be neglected. To overcome drawbacks of the simple transit time analysis, we use 2D device simulations to obtain an improved understanding of the measured high-frequency parameters. Taking into account the real doping profiles and device structures, and using a calibrated parameter set for strained SiGe, the simulation results for the Si, Si1-xGex, and Si1-yCy (y less than or equal to 0.2%) base layer transistors reproduce very well the measured transit times (assuming the Si data for the electron mobility mu(n)) in the heteroepiaxial base layers. In the case of higher carbon concentration (y = 1%), the electron mobility is reduced by a factor of two.