Hi,
You will claim points as per assessment done by the "designated organizations for ECAs" - ICAS, WES, CES etc.
If you submitted your Masters and it was assessed as equivalent to Canadian Masters, then you can claim points as follows:
Express Entry Comprehensive Ranking System (with spouse) 126
Express Entry Comprehensive Ranking System (without spouse) 135
Federal Skilled Worker Program factor points (if this applies) 23
If you submitted your Masters and it was assessed as equivalent to Canadian Bachelors, then you can claim points as follows:
Express Entry Comprehensive Ranking System (with spouse) 112
Express Entry Comprehensive Ranking System (without spouse) 120
Federal Skilled Worker Program factor points (if this applies) 21
In a nut shell, regardless of what degree you hold, you claim points based on the assessment you received from the designated organizations for ECAs.
http://www.cic.gc.ca/english/immigrate/skilled/assessment.asp
Good Luck.