Not Updated For Current Season
The masteries shown here are not yet updated for the current season, the guide author needs to set up the new masteries. As such, they will be different than the masteries you see in-game.
Ive recent started playing malzahar, and ive had plenty of success with him. He does some serious work.
You should always mid with malz (or solo on a 3v).
The core items of this build are Archangels, Zhonyas, and Rylai's. After you hit this point, you're rocking around 400ap. Then i get hextech revolver because some spellvamp keeps you rocking in teamfights.
Your final item is up to you, i prefer abyssal, because it lowers their resistance, and combine that with your magic pen runes + boots, you are going to be putting in some work.
Comments are appreciated. I included the exact buying path i use when i play him. This may or may not work for you.
Oh, and of course, before you use your ult, throw down your W. After your high AP, youre going to be doing 14-15% of their hp/second. Combine that with your ult which will do 1200 or so (over 2.5 seconds), you do (14% * 2.5) + 1200 = nuke on anyone.