Here is the full list of all 41 Prototype trophies - there are 26 bronze, 10 silver, 4 gold and 1 platinum.
Platinum Trophy
Complete Story Mode on hard difficulty.
Kill 53,596 infected.
Acquire all nodes of the Web of Intrigue.
Discover the history of Elizabeth Greene through the Web of Intrigue.
Discover what happened to Alex Mercer through the Web of Intrigue.
Complete all Consume Events.
Acquire all available upgrades.
Discover the truth behind Hope, Idaho through the Web of Intrigue.
Achieve a Platinum Medal in all Events.
Achieve a rating of Gold or better in all Events.
Complete the game while consuming 10 Civilians or fewer.
Complete Story Mode in any difficulty without dying.
Complete the Supreme Hybrid Boss Battle.
Complete the Mother Boss Battle.
Complete 3 missions without causing a single Military Alert.
Catch any object tossed by a Hydra; and throw it back.
Destroy 10 Military Bases or Infected Hives in New York City.
Shoot down 50 helicopters while driving armor.
Destroy 2,000 vehicles.
Destroy 25 strike teams.
Seize 50 vehicles from enemy hands.
Patsy 5 military personnel.
Kill 50 characters in 5 seconds.
Infiltrate 10 Military Bases disguised as a Commander.
Evade 10 strike teams.
Destroy 20 Helicopters in a single Helicopter flight.
Complete the Supreme Hunter Boss Battle.
Destroy 25 Infected Water Towers before they hatch.
Kill 15 characters with a single Whipfist attack.
Consume 50 Web Targets.
Collect all Landmark collectibles scattered across New York City.
Gain the ability to drive and fly all vehicles.
Complete a mission without causing a single Military Alert.
Consume 200 characters to boost your health.
Complete the Specialist Boss Fight.
Run over 500 characters in a single tank.
Complete the Hunter Boss Encounter.
Collect all Hint Collectibles scattered across New York City.
Use the Upgrade Menu to acquire an Upgrade.
Unlock the Web of Intrigue.