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