What kind of MS data ? There's plenty of software for different types of data/tasks. You can start by having a look on OMICtools or at the list of MS software on wikipedia.

If you are not afraid to install some tools, you can take a look to open source software as OpenMS, OpenSwath. To process mzML data I used OpenSwathWorkflow and TOPPview for mzML visualisation. For general analysis you can take a look to TPP software (Trans-Proteomic Pipeline).

Hey,

In my opinion, MaxQuant is the best and most used, it is quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets.

Best regards,

Leite

As it has been said, the software tools depend on the type of analyses you want to do. Maybe Mass-Up (http://www.sing-group.org/mass-up/; https://doi.org/10.1186/s12859-015-0752-4) can be useful to you if you want to preprocess raw spectra and perform clustering analysis or PCA in the peak lists.