Malzahar is one of the strongest AP carries that can 1v1 anyone. He has the ability to silence, suppress, whip out a lot of damage over time and an ability to destroy high HP targets. Malzahar is not like any other AP carry where you just throw things, he requires A LOT OF positioning to be a strong hero. Malzahar's silence allows for great poking power and strong initiating. He can destroy other carries with his strong position and suppression allowing your team to hop on them and obliterate them. Malzahar can kill anyone he pleases to kill even if it is a tank or a support. Malzahar can knock out important enemy champions out of the fight.

Marks

Magic penetration are the best marks as an AP carry. They allow you to do decent damage early game, and when paired up with Sorcerer's Shoes, you have the 30 magic penetration required to deal true magic damage to many non-tank targets.

Seals

For seals, you'll want to use scaling mana regeneration to allow more ability spamming. The mana sustain helps your early game due to Malzahar's poor early mana regeneration. You want to take the scaling runes over the flats because they are superior to them as early as level 5.

Glyphs

Flat ability power glyphs will give you the upper hand in early game with your poke.

Quintessences

Flat ability power quints are preferable over scaling AP quintessences, as the level crossover is too high for them to be valuable. The flats are the best in slot for most AP Carries.

I go with the Masteries 23/0/8. Getting the ability power and magic penetration from the offensive tree and the mana and mana regen from the utility tree. This will help your early game out with increased damage and with the bonus mana and mana regen, being able to stay in lane longer.

For items, I like to rush for a Athene's Unholy Grail for its Mana Regeneration and the Cooldown Reduction it give. Then getting the Archangel's Staff so you won't have to go back as often and if you get it to Seraph's Embrace, it can be useful in team fights for staying in for a little longer. Then you start to build your items that'll give you Magic Penetration and tons of Ability Power. And if you complete the build Elixirs and an Oracle never hurt.

I find the best skill sequence is w q e r because you want them in that null zone for as much time as possible + with the q silence, champs like Olaf will have their ult delayed and then the e for the extra damage and the ult to suppress the enemy. If the champ is caught alone and you land all your skills, you should be able to kill most champs even at full hp. I find this to be the most effective skill sequence for optimal damage output.

I think the spells Ignite and Flash work best for Malzahar but ghost works too. I like to have ignite for those last minute flashes over walls or even flashing into fights to burst down the adc and Ignite is always a nice spell to have to help take down enemies with that deadly combo.