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