M.S is the abbreviation of Master of Science and M.Eng is the abbreviation of Master of Engineering.
Some universities offer M.S while others offer M.Eng. Both are master's course and can be used to enhance the boundaries of one's knowledge in a field. M.S is more of a research oriented course while M.Eng has more of a course-work based curriculum. Finally, it is up to an individual to decide whether he would like to do a M.S or M.Eng degree.
Note: Some universities offer S.M degree instead of M.S (Both are basically the same!).
