Patent ID: 6958473

Claim:
A method of enhanced biomarker detection using data directed mass filtering comprising the steps of: selecting an ion trap mass analyzer and an ion filter; introducing a first separation run of ions from a separation device and ionization source into the ion filter and followed by the ion trap mass analyzer which includes an ion trap and a detector; accumulating at least a portion of the first separation of ions within the ion trap for an initial period of time for subsequent ion detection by the detector; measuring mass to charge (m/z) values for a mass spectrum corresponding to desired ion species and undesired ion species contained in the first separation run of ions; measuring elution times for ions of interest within the first separation run eluted from the separation device to determine a priori retention time intervals for ions of interest; introducing a second separation run of ions through the separation device and into the ion filter; measuring elution times for the second separation run of ions to determine whether they fall within at least one a priori determined retention time interval for ions of interest so only ions of interest are filtered and pass from the ion filter into the ion trap to notch out portions of the mass spectrum corresponding to undesired ions; and accumulating only the ions of interest within the second separation run of ions in the ion trap for a predetermined period of time that is derived at least in part by measured intensities of the ions of interest in the first separation run of ions, and wherein the predetermined period of time does not exceed a priori retention time intervals for ions of interest determined during the first separation run.