Q Exactive plus is an excellent instrument for both experimental approaches, plus there are powerful frameworks to deal with the data analysis (e.g. OpenMS / MaxQuant / Skyline).

WIth MALDI you are limited with the pre-ms fractionation. You can couple the Q Exactive with a high pressure nano LC and get reasonable proteome coverage using 60-120 min LC gradients. This is not possible with MALDI while a MALDI target spotter would not get close to high pressure nano LC thus MALDI would limit your proteome coverage.

Resolution and sensitivity also come into play as the Q Exactive is probably better on both accounts, while a modern TOF can be faster.