How do I Run multiple protractor test suites at once?

Don't put spaces after commas:

protractor config.js --suite rf1_breast,rf1_ovarian,rf1_pancreatic

In your config.js

If you want to run the script as a suite comment out the spec line

// specs: ['src/com/sam/scriptjs/alertexamplespec.js']

give the suite name and location

 suites: {
      //Suite name and location give * to run all the specs or provide the name 
        smoke: ['./smoke/*.spec.js'],
        endtoend: ['src/com/sam/scriptjs/*.spec.js'],
//Futhermore you can select few test specs
testfew: ['./smoke/editorder.spec.js','./smoke/cancelorder.spec.js']

},  

then in cmd type protractor filenameconfig.js