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