I could not add the 1098-E in the federal section since I indicated that I am married filing separately. There does not seem to be a provision excluding deducting student loan interest for Massachusetts based on filing status. The online edition does not seem to have the same limitation.
No. The student loan interest deduction for the state of Massachusetts is based on the qualified federal deduction and is not allowed if you did not claim the interest on your federal return.
Massachusetts General Rule:
Massachusetts allows 2 student loan interest deductions for interest paid on a "qualified education loan":
Please view the Student Loan Interest Deduction section in the Massachusetts link below for more information.
https://www.mass.gov/service-details/learn-about-education-related-deduction