Answer:
"An MA thesis" is correct.
Explanation:
The choice between "a" or "an" depends on whether the following word starts with a consonant or vowel sound:
If the following word begins with a vowel sound then use "an", otherwise use "a".
Note that the choice is based on the sound of the following word rather than its first letter.
The abbreviation "MA" starts with a vowel sound, like "em", so we use "an" rather than using "a".