A method for tracking entities in an LC/MS system, comprising: a) injecting a sample into a liquid chromatograph to separate entities in the sample and to determine a retention time associated with each entity; b) inputting the entities into a mass spectrometer to determine a mass for each entity; c) choosing a subset of entities having intensities higher than a predetermined threshold from a first injection and choosing a subset of entities having intensities higher than a predetermined threshold from a second injection, wherein the thresholds in each of said first and second injections include a mass threshold and a coarse retention time threshold; d) conducting a search to compare all threshold selected entities chosen from the first injection to those chosen from the second injection; e) identifying entities chosen from the first injection that match entities chosen from the second injection using the mass threshold and coarse retention time threshold; characterized in that the method further comprises: f) constructing a retention time map based on the matching entities; g) assigning reference retention times based on the retention time map to the matching entities from the first and second injections; h) utilizing the occurrence of regularities relating to reference retention times and retention time order of entities in said first and said second injection so as to assign reference retention times to entities not included in said retention time map, whereby the assignment of reference retention times to each of said entities within said first and/or said second injection removes the retention time offset between entities in said injections; and i) tracking entities through the first and second injections using the reference retention times and mass threshold so that any quantitative change in concentration of an entity in a sample is measured. a) injecting a sample into a liquid chromatograph to separate entities in the sample and to determine a retention time associated with each entity; b) inputting the entities into a mass spectrometer to determine a mass for each entity; c) choosing a subset of entities having intensities higher than a predetermined threshold from a first injection and choosing a subset of entities having intensities higher than a predetermined threshold from a second injection, wherein the thresholds in each of said first and second injections include a mass threshold and a coarse retention time threshold; d) conducting a search to compare all threshold selected entities chosen from the first injection to those chosen from the second injection; e) identifying entities chosen from the first injection that match entities chosen from the second injection using the mass threshold and coarse retention time threshold; f) constructing a retention time map based on the matching entities; g) assigning reference retention times based on the retention time map to the matching entities from the first and second injections; h) utilizing the occurrence of regularities relating to reference retention times and retention time order of entities in said first and said second injection so as to assign reference retention times to entities not included in said retention time map, whereby the assignment of reference retention times to each of said entities within said first and/or said second injection removes the retention time offset between entities in said injections; and i) tracking entities through the first and second injections using the reference retention times and mass threshold so that any quantitative change in concentration of an entity in a sample is measured.