Here, we demonstrated that with a low RF frequency convex TIMS cartridge, we were able to mobility-separate charge-reduced 3 and 4 MDa T=3 and T=4 HBV capsids. A single charge state of chargereduced GroEL could be quadrupole-selected at m/z 16,200 with a 25 m/z isolation window with the low RF frequency quadrupole driver. Also, a 2-lens SID device was able to fragment 801 kDa GroEL and investigate its subunit connectivity. The MS/MS fragments cover a wider m/z range under a single set of tuning conditions than previously reported for other instrument platforms. Significantly, the peaks of fragments at high m/z are relatively narrow and well resolved, which improves the identification of different subcomplexes. The SID device also replaces the preexisting entrance lens of the collision cell, requiring no hardware modifications and relatively simple installation. SID can also be used as a tool to probe the structural information of ions of The detection limit of this instrument is also outstanding. We were able to perform nMS for HBV capsids in the concentration range of 20 to 50 nM. Moreover, with ion mobility separation prior to the quadrupole isolation and SID fragmentation, when characterizing a specific protein complex from a complex mixture using nMS, we were able to differentiate those SID products from the m/z overlapping precursors. The fragments were mobility-aligned with their precursor, which simplifies the interpretation of SID products to study their subcomplex arrangement and connectivity.