This is not... strictly true. Assuming mass is no object,
We derive true damage rates for armor and shields by doing the (Shields + Armor/4) or (Armor + Shields/4) calculation and multiplying it by shots per second produced by the weapon (60/Reload). As such,
Laser Cannon
Armor/Sec: 13.5
Shield/Sec: 31.5
Proton Cannon
Armor/sec: 25.0
Shield/Sec: 25.0
This is because the proton cannon strobes twice a second, while the laser cannon strobes three times a second. The proton's additional massdamage is enough to offset this against armor, but not against shields. Turrets, however, are a little dicier:
Laser Turret
Armor/Sec: 15.0
Shield/Sec: 60.0
Proton Turret
Armor/Sec: 75.0
Shield/Sec: 75.0
This is because there are two laser cannons on a laser turret, while there are three proton cannons on a proton turret. So when we get to this level, the strobe rates are effectively identical and the proton cannon's better mass damage prevails, and even bleeds into shield damage a little.
Of course, the aliens have no armor, so you should only pay attention to the shield/sec numbers> To me these suggest that you should stock up on proton turrets and laser cannons.
This doesn't take mass into consideration, but sine you'll won't be able to use other secondaries while running your tractor beam, it hardly matters in this instance.
-reg
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"Oh crap. I'm going to hell - I put the Bible next to Mein Kampf again."
-Her Holiness, Pope Jenne "Kirby" Hubbs