The theory of quantum trajectories is applied to simulate the effects of quantum noise sources induced by the environment on quantum information protocols. We study two models that generalize single qubit noise channels like amplitude damping and phase flip to the many-qubit situation. We calculate the fidelity of quantum information transmission through a chaotic channel using the teleportation scheme with different environments. In this example, we analyze the role played by the kind of collective noise suffered by the quantum processor during its operation. We also investigate the stability of a quantum algorithm simulating the quantum dynamics of a paradigmatic model of chaos, the baker's map. Our results demonstrate that, using the quantum trajectories approach, we are able to simulate quantum protocols in the presence of noise and with large system sizes of more than 20 qubits.