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