In a future ATM system, Trajectory Based Operations (TBO) is considered to be one of the key concepts required to meet the ever increasing demand for air transportation. Information on aircraft mass and weather conditions are key to precise performance modeling and benefits estimation in a TBO environment. This paper quantitatively discusses this issue by estimating weather conditions and fuel consumption from surveillance data, numerical weather predictions and BADA aircraft performance model data, and reviewing modeling errors by comparison with actual flight data. Also, a trajectory optimization model based on the dynamic programming method is applied to discuss variations in potential benefits estimation. Preliminary results show that initial mass values are highly varied between actual and reference mass values according to subjected operational scenarios. Estimations of weather data show that numerical weather forecast data are sufficiently accurate to be utilized in off-line performance estimation. Fuel consumption calculations show that mass variations have significant impacts on performance estimation in each phase of flight. Optimization results show up to a 7% difference in the estimates of potential fuel savings with respect to initial mass difference ranging between 0% and 40%. Optimization with free arrival time constraints result in flight time differences of between -8% to 2% with respect to the above initial mass difference.