Brooks Automation Inc., a Chelmsford provider of automation, vacuum, and instrumentation products for such markets as the semiconductor industry, will cut 100 jobs, or 6 percent, of its workforce as it looks to “achieve cost synergies” and increase profits.

The company said Wednesday that 29 of the jobs being cut are in Massachusetts. Brooks will be left with a Bay State head count of 605. Brooks recently acquired Crossing Automation Inc.