Mass spectrometry (MS) has been recognized as a powerful technique to detect accurate chemical information about metal clusters. Maintaining metal clusters intact, which is a great challenge in MS analysis, was achieved in this work by choosing a suitable mass analyzer and carefully optimizing analysis parameters. Electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS) and electrospray ion trap mass spectrometry (ESI-IT-MS) were applied to characterize the synthesized ligand-protected metal clusters [Au6 Ag2 (C)(L(1) )6 ](BF4 )4 (L(1) =2-diphenylphosphanyl-4-methylpyridine) (1) and [Au8 (L(2) )3 (L(3) )2 ](NO3 )2 (L(2) =bis(2-diphenylphosphinophenyl)ether, L(3) =triphenyl-phosphane) (2). Three kinds of buffer gas (helium, mass: 2; nitrogen, mass: 28; argon, mass: 40) and various radiofrequency (RF) amplitudes (from 70 to 330) were chosen to study the fragmentation rate during the "collision cooling" process in the ion trap analyzer. In the ESI-TOF-MS analysis, metal clusters 1 and 2 were mainly observed as intact clusters, which were Au6 Ag2 (C)(L(1) )6 (BF4 )2 (2+) , Au6 Ag2 (C)(L(1) )6 (BF4 )(3+) , Au6 Ag2 (C)(L(1) )6 (4+) for 1 and Au8 (L(2) )3 (L(3) )2 (2+) for 2. While, in the ESI-IT-MS analysis, only fragments could be found, such as Au6 Ag(C)(L(1) )6 (BF4 )(2+) , Au6 (C)(L(1) )6 (2+) , Au5 Ag(C)(L(1) )4 (2+) , Au6 Ag(C)(L(1) )6 (3+) , Au(L(1) )(+) for 1 and Au8 (L(2) )3 (L(3) )(2+) , Au8 (L(2) )3 (2+) , Au6 (L(2) )3 (2+) for 2. It is obvious that the two kinds of mass analyzers caused different MS behaviors of metal clusters. In the ion trap (IT) mass analyzer, particularly, "collision cooling" was contributing to further dissociation of fragile compounds, in which a higher RF amplitude and a larger mass buffer gas led to more fragmentation. In this work, intact metal clusters were obtained in ESI-TOF-MS, instead of ESI-IT-MS, in which the "collision cooling" process caused more cluster dissociation. It was concluded that the analyzer in ESI-TOF-MS is "softer" than that in ESI-IT-MS for metal clusters. Copyright © 2016 John Wiley & Sons, Ltd.