# US RE50,171 E1 · Automated analysis of complex matrices using mass spectrometer > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US RE50,171 E1 - Document ID: USRE50171E1 - Status: Granted - Kind: E1 - Application number: 17/682,960 - Filed: 2022-02-28 - Granted: 2024-10-15 - Earliest claimed: 2005-12-07 - Assignees: DH Technologies Development Pte. Ltd. - Applicants: Dh Technologies Development Pte. Ltd. - Inventors: Byron Kieser - Web page: https://patentgrep.com/patent/USRE50171E1 ## CPC - B01D 59/44: Separation by mass spectrography (particle spectrometers or separator tubes H01J49/00) - B01D: SEPARATION (separating solids from solids by wet methods B03B, B03D; by pneumatic jigs or tables B03B; by other dry methods B07; magnetic or electrostatic separation of solid materials from solid materials or fluids, separation by high-voltage electric fields B03C; centrifuges, vortex apparatus B04; presses per se for squeezing-out liquid from liquid-containing material B30B9/02; treatment of water C02F, e.g. softening by ion-exchange C02F1/42; {arrangements of air intake cleaners in gas turbine plants F02C7/05} ; arrangements or mounting of filters in air-conditioning, air-humidification or ventilation F24F13/28) ## Abstract Improved systems, apparatus, methods, and programming useful for the automated analysis of complex compounds using mass spectrometers. Systems, apparatus, methods, and programming according to the invention provide for the automatic determination by a controller 54 of a mass spectrometer 14, 214 of an analysis operation to be implemented using the mass spectrometer, the analysis operation adapted specifically for analysis of one or more substances based contained within a compound based on identification of the compound and/or substances provided by a user of the spectrometer, and a database 66 or other library of information concerning suitable processes or process steps for analyzing substances. ## Claims ### Claim 1 A method of controlling a mass spectrometer in the analysis of a compound, the method performed by a controller of an automated mass analyzer and comprising: receiving from an input source signals representing an identifier identifying a the compound comprising a plurality of substances; using the identifier, automatically accessing data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determining a set of command signals for use by a the mass spectrometer in analyzing at least a portion of the compound; and providing the command signal set to the mass spectrometer, in order to configure the mass spectrometer to analyze at least a portion of the compound, wherein the method is performed by the controller of the automated mass analyzer comprising a compound source adapted to provide the compound over a period of time, wherein: the method includes the controller receiving a designation identifying a range of times within which portions of the compound are to be provided by the compound source to the mass spectrometer; and the command signal set determined by the controller using the accessed data set and the identified time range is adapted to cause the mass spectrometer to perform multiple scan duty cycles, the respective duty cycles adapted for detecting ions associated with the identifier in accordance with a time at which the ions are to be provided by the compound source. ### Claim 2 (depends on 1) The method of claim 1, performed by a controller of an automated mass analyzer comprising a compound source adapted to provide a compound over a period of time, wherein: the method includes the controller receiving a designation identifying a range of times within which portions of the compound are to be provided by the compound source to the mass spectrometer; and the command signal set determined by the controller using the accessed data set and the identified time range is adapted to cause the mass spectrometer to perform multiple scan duty cycles, the respective duty cycles adapted for detecting ions associated with the identifier in accordance with a time at which the ions are to be provided by the compound source. ### Claim 3 (depends on 2) The method of claim 2 1, wherein the designation identifying a range of times comprises at least one specified time and a time range tolerance. ### Claim 4 (depends on 1) The method of claim 1 3, wherein the mass analyzer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device, and the analysis parameters associated with the identifier comprise data useable by the controller for automatically determining command signals adapted for controlling at least one the multiple scan duty cycle cycles performed by the mass spectrometer in analyzing the compound. ### Claim 5 (depends on 4) The method of claim 4, wherein the multiple scan duty cycle comprises cycles comprise a portion of a Multiple Reaction Monitoring (MRM) or Enhanced Product Ion (EPI) analysis. ### Claim 6 A system useful for the automated analysis of compounds using a mass spectrometer, the system comprising: a the mass spectrometer adapted to receive ions from ion source, a controller adapted to receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; to use the identifier to automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, to automatically determine a set of command signals for use by a mass spectrometer in analyzing at least a portion of the compound; and to provide output signals representing the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing at least a portion of the compound. ### Claim 7 (depends on 6) The system of claim 6, wherein the controller is adapted in accordance with instructions of a control program stored in a memory associated with the controller. ### Claim 8 (depends on 7) The system of claim 7, wherein the memory is volatile or persistent. ### Claim 9 A computer usable medium having computer readable code embodied therein for causing a controller for a mass analysis system to: receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; using the identifier, automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determine a set of command signals for use by a mass spectrometer in analyzing at least a portion of the compound; and provide the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing at least a portion of the compound. ### Claim 10 (depends on 9) The computer usable medium of claim 9, wherein the computer readable code is further configured to cause the controller to: receive a designation identifying a specified time and a time range tolerance in which portions of the compound are to be provided by a compound source to the mass spectrometer; and cause the mass spectrometer to perform multiple scan duty cycles, wherein respective duty cycles are adapted for detecting ions associated with the identifier in accordance with a time at which the ions are to be provided by the compound source, and wherein the multiple scan duty cycles comprise a portion of a Multiple Reaction Monitoring (MRM) analysis. ### Claim 11 (depends on 10) The computer usable medium of claim 10, wherein the computer readable code is configured to cause the controller to receive the designation identifying the specified time and the time range tolerance from at least one of an input device operated by a user and a data store communicatively coupled with the controller. ### Claim 12 (depends on 6) The system of claim 6, wherein the controller is further adapted to receive a designation identifying a specified time and a time range tolerance in which portions of the compound are to be provided by a compound source to the mass spectrometer; and cause the mass spectrometer to perform multiple scan duty cycles, wherein respective duty cycles are adapted for detecting ions associated with the identifier in accordance with a time at which the ions are to be provided by the compound source, and wherein the multiple scan duty cycles comprise a portion of a Multiple Reaction Monitoring (MRM) analysis. ### Claim 13 (depends on 12) The system of claim 12, wherein the controller is further adapted to receive the designation identifying the specified time and the time range tolerance from at least one of an input device operated by a user and a data store communicatively coupled with the controller. ### Claim 14 (depends on 3) The method of claim 3, wherein the designation identifying the specified time and the time range tolerance is received from at least one of an input device operated by a user and a data store communicatively coupled with the controller. ### Claim 15 A method of controlling a mass spectrometer in a Multiple Reaction Monitoring (MRM) analysis of a compound, the method performed by a programmed controller of an automated mass analyzer and comprising: receiving from an input source signals representing an identifier identifying a compound comprising a plurality of substances; receiving at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; using the identifier, automatically accessing data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determining a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and providing the command signal set to the mass spectrometer, in order to configure the mass spectrometer to analyze the portion of the compound by applying one or more voltages to the mass spectrometer such that, at each of a plurality of time points during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with at least one of the plurality of substances when the time point is within the respective time range tolerance identified for the at least one of the plurality of substances. ### Claim 16 (depends on 15) The method of claim 15, wherein the at least one designation identifying the specified time and the time range tolerance is received from at least one of an input device operated by a user and a data store communicatively coupled with the programmed controller. ### Claim 17 (depends on 15) The method of claim 15, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 18 (depends on 15) The method of claim 15, wherein the identifier identifies parent-daughter transitions of interest. ### Claim 19 (depends on 15) The method of claim 15, wherein the identifier identifies toxins or drugs of abuse for screening of a biological sample. ### Claim 20 (depends on 15) The method of claim 15, wherein the identifier identifies pesticide residues for screening of a food, beverage, or environmental sample. ### Claim 21 (depends on 15) The method of claim 15, wherein the plurality of substances analyzed in the compound is greater than 100. ### Claim 22 (depends on 15) The method of claim 15, further comprising adjusting the command signal set applied to the mass spectrometer in at least one scan cycle of a plurality of scan cycles based on data generated by the mass spectrometer in an earlier scan cycle to at least one of: i) confirm one or more substances identified in the earlier scan cycle, and ii) correct for variations in elution time from the LC column. ### Claim 23 A system for the automated MRM analysis of compounds, the system comprising: a mass spectrometer adapted to receive ions from an ion source, a controller adapted to: receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; receive at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; use the identifier to automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determine a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and provide output signals representing the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing the portion of the compound such that, at each of a plurality of time points during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with at least one of the plurality of substances when the time point is within the respective time range tolerance identified for the at least one of the plurality of substances. ### Claim 24 (depends on 23) The system of claim 23, wherein the command signal set controls one or more voltages applied to the mass spectrometer. ### Claim 25 (depends on 24) The system of claim 24, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 26 A method of controlling a mass spectrometer in a Multiple Reaction Monitoring (MRM) analysis of a compound, the method performed by a programmed controller of an automated mass analyzer and comprising: receiving from an input source signals representing an identifier identifying the compound comprising a plurality of substances; receiving at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; using the identifier, automatically accessing data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determining a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and providing the command signal set to the mass spectrometer, in order to configure the mass spectrometer to analyze the portion of the compound by applying one or more voltages to the mass spectrometer such that for each of a plurality of scan cycles during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with one or more selected substances of the plurality of substances when the scan cycle occurs within the respective time range tolerance identified for the one or more selected substances. ### Claim 27 (depends on 26) The method of claim 26, wherein the at least one designation identifying the specified time and the time range tolerance is received from at least one of an input device operated by a user and a data store communicatively coupled with the programmed controller. ### Claim 28 (depends on 26) The method of claim 26, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 29 (depends on 26) The method of claim 26, wherein the identifier identifies parent-daughter transitions of interest. ### Claim 30 (depends on 26) The method of claim 26, wherein the identifier identifies toxins or drugs of abuse for screening of a biological sample. ### Claim 31 (depends on 26) The method of claim 26, wherein the identifier identifies pesticide residues for screening of a food, beverage, or environmental sample. ### Claim 32 (depends on 26) The method of claim 26, wherein the plurality of substances analyzed in the compound is greater than 100. ### Claim 33 (depends on 26) The method of claim 26, further comprising adjusting the command signal set applied to the mass spectrometer in at least one scan cycle of the plurality of scan cycles based on data generated by the mass spectrometer in an earlier scan cycle to at least one of: i) confirm one or more substances identified in the earlier scan cycle, and ii) correct for variations in elution time from the LC column. ### Claim 34 A system for the automated MRM analysis of compounds, the system comprising: a mass spectrometer adapted to receive ions from an ion source, a controller adapted to: receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; receive at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; use the identifier to automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determine a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and provide output signals representing the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing the portion of the compound such that for each of a plurality of scan cycles during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with one or more selected substances of the plurality of substances when the scan cycle occurs within the respective time range tolerance identified for the one or more selected substances. ### Claim 35 (depends on 34) The system of claim 34, wherein the command signal set controls one or more voltages applied to the mass spectrometer. ### Claim 36 (depends on 35) The system of claim 35, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 37 A method of controlling a mass spectrometer in a Multiple Reaction Monitoring (MRM) analysis of a compound, the method performed by a programmed controller of an automated mass analyzer and comprising: receiving from an input source signals representing an identifier identifying the compound comprising a plurality of substances; receiving at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; using the identifier, automatically accessing data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determining a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and providing the command signal set to the mass spectrometer, in order to configure the mass spectrometer to analyze the portion of the compound for a plurality of scan cycles by adjusting one or more voltages applied to the mass spectrometer, wherein the command signal set is configured to adjust which individual selective scans are performed in each scan cycle based on the at least one designation identifying the specified time and the time range tolerance in which each substance would be expected to be received from the LC column. ### Claim 38 (depends on 37) The method of claim 37, wherein the command signal set is configured to operate the mass spectrometer such that, at each of a plurality of time points during the MRM analysis, an individual selective scan is performed for at least one of the plurality of substances when the time point is within the respective time range tolerance identified for the at least one of the plurality of substances. ### Claim 39 (depends on 37) The method of claim 37, wherein the command signal set is configured to operate the mass spectrometer such that for each scan cycle during the MRM analysis, an individual selective scan for one or more selected substances of the plurality of substances is performed when the scan cycle occurs within the respective time range tolerance identified for the one or more selected substances. ### Claim 40 (depends on 37) The method of claim 37, wherein the at least one designation identifying the specified time and the time range tolerance is received from at least one of an input device operated by a user and a data store communicatively coupled with the programmed controller. ### Claim 41 (depends on 37) The method of claim 37, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 42 (depends on 37) The method of claim 37, wherein the identifier identifies parent-daughter transitions of interest. ### Claim 43 (depends on 37) The method of claim 37, wherein the identifier identifies toxins or drugs of abuse for screening of a biological sample. ### Claim 44 (depends on 37) The method of claim 37, wherein the identifier identifies pesticide residues for screening of a food, beverage, or environmental sample. ### Claim 45 (depends on 37) The method of claim 37, wherein the plurality of substances analyzed in the compound is greater than 100. ### Claim 46 (depends on 37) The method of claim 37, further comprising adjusting the command signal set applied to the mass spectrometer in at least one scan cycle of the plurality of scan cycles based on data generated by the mass spectrometer in an earlier scan cycle to at least one of: i) confirm one or more substances identified in the earlier scan cycle, and ii) correct for variations in elution time from the LC column. ### Claim 47 A system for the automated MRM analysis of compounds, the system comprising: a mass spectrometer adapted to receive ions from an ion source, a controller adapted to: receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; receive at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; use the identifier to automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determine a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and provide output signals representing the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing the portion of the compound for a plurality of scan cycles, wherein the command signal set is configured to adjust which individual selective scans are performed in each scan cycle based on the at least one designation identifying the specified time and the time range tolerance in which each substance would be expected to be received from the LC column. ### Claim 48 (depends on 47) The system of claim 47, wherein the command signal set controls one or more voltages applied to the mass spectrometer. ### Claim 49 (depends on 48) The system of claim 48, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 50 A method of controlling a mass spectrometer in a Multiple Reaction Monitoring (MRM) analysis of a compound, the method performed by a programmed controller of an automated mass analyzer and comprising: receiving from an input source signals representing an identifier identifying the compound comprising a plurality of substances; receiving at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; using the identifier, automatically accessing data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determining a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and providing the command signal set to the mass spectrometer, in order to configure the mass spectrometer to analyze the portion of the compound for a plurality of scan cycles by applying one or more voltages to the mass spectrometer, wherein a duty cycle of each scan cycle is based on the at least one designation identifying the specified time and the time range tolerance in which each of the plurality of substances would be expected to be received from the LC column. ### Claim 51 (depends on 50) The method of claim 50, wherein the command signal set is configured to operate the mass spectrometer such that, at each of a plurality of time points during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with at least one of the plurality of substances when the time point is within the respective time range tolerance identified for the at least one of the plurality of substances. ### Claim 52 (depends on 50) The method of claim 50, wherein the command signal set is configured to operate the mass spectrometer such that for each scan cycle during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with one or more selected substances of the plurality of substances when the scan cycle occurs within the respective time range tolerance identified for the one or more selected substances. ### Claim 53 (depends on 50) The method of claim 50, wherein the at least one designation identifying the specified time and the time range tolerance is received from at least one of an input device operated by a user and a data store communicatively coupled with the programmed controller. ### Claim 54 (depends on 50) The method of claim 50, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 55 (depends on 50) The method of claim 50, wherein the identifier identifies parent-daughter transitions of interest. ### Claim 56 (depends on 50) The method of claim 50, wherein the identifier identifies toxins or drugs of abuse for screening of a biological sample. ### Claim 57 (depends on 50) The method of claim 50, wherein the identifier identifies pesticide residues for screening of a food, beverage, or environmental sample. ### Claim 58 (depends on 50) The method of claim 50, wherein the plurality of substances analyzed in the compound is greater than 100. ### Claim 59 (depends on 50) The method of claim 50, further comprising adjusting the command signal set applied to the mass spectrometer in at least one scan cycle of the plurality of scan cycles based on data generated by the mass spectrometer in an earlier scan cycle to at least one of: i) confirm one or more substances identified in the earlier scan cycle, and ii) correct for variations in elution time from the LC column. ### Claim 60 A system for the automated MRM analysis of compounds, the system comprising: a mass spectrometer adapted to receive ions from an ion source, a controller adapted to: receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; receive at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; use the identifier to automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determine a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and provide output signals representing the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing the portion of the compound for a plurality of scan cycles, wherein the command signal set is configured to adjust a duty cycle of each scan cycle based on the at least one designation identifying the specified time and the time range tolerance in which each of the plurality of substances would be expected to be received from the LC column. ### Claim 61 (depends on 60) The system of claim 60, wherein the command signal set controls one or more voltages applied to the mass spectrometer. ### Claim 62 (depends on 61) The system of claim 61, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 63 A method of controlling a mass spectrometer in a Multiple Reaction Monitoring (MRM) analysis of a compound, the method performed by a programmed controller of an automated mass analyzer and comprising: receiving from an input source signals representing an identifier identifying the compound comprising a plurality of substances; receiving at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; using the identifier, automatically accessing data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determining an optimal duty cycle for each of the plurality of substances based on the at least one designation and a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and providing the command signal set to the mass spectrometer, in order to configure the mass spectrometer to analyze the portion of the compound based on the optimal duty cycles by adjusting one or more voltages applied to the mass spectrometer. ### Claim 64 (depends on 63) The method of claim 63, wherein the command signal set is configured to operate the mass spectrometer such that, at each of a plurality of time points during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with at least one of the plurality of substances when the time point is within the respective time range tolerance identified for the at least one of the plurality of substances. ### Claim 65 (depends on 63) The method of claim 63, wherein the command signal set is configured to operate the mass spectrometer such that for each scan cycle during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with one or more selected substances of the plurality of substances when the scan cycle occurs within the respective time range tolerance identified for the one or more selected substances. ### Claim 66 (depends on 63) The method of claim 63, wherein the at least one designation identifying the specified time and the time range tolerance is received from at least one of an input device operated by a user and a data store communicatively coupled with the programmed controller. ### Claim 67 (depends on 63) The method of claim 63, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 68 (depends on 63) The method of claim 63, wherein the identifier identifies parent-daughter transitions of interest. ### Claim 69 (depends on 63) The method of claim 63, wherein the identifier identifies toxins or drugs of abuse for screening of a biological sample. ### Claim 70 (depends on 63) The method of claim 63, wherein the identifier identifies pesticide residues for screening of a food, beverage, or environmental sample. ### Claim 71 (depends on 63) The method of claim 63, wherein the plurality of substances analyzed in the compound is greater than 100. ### Claim 72 (depends on 63) The method of claim 63, further comprising adjusting the command signal set applied to the mass spectrometer in at least one scan cycle of a plurality of scan cycles based on data generated by the mass spectrometer in an earlier scan cycle to at least one of: i) confirm one or more substances identified in the earlier scan cycle, and ii) correct for variations in elution time from the LC column. ### Claim 73 A system for the automated MRM analysis of compounds, the system comprising: a mass spectrometer adapted to receive ions from an ion source, a controller adapted to: receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; receive at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each of the plurality of substances would be expected to be received from a LC column associated with the mass spectrometer; use the identifier to automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determine an optimal duty cycle for each of the plurality of substances based on the at least one designation and a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and provide output signals representing the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing the portion of the compound based on the optimal duty cycles. ### Claim 74 (depends on 73) The system of claim 73, wherein the command signal set controls one or more voltages applied to the mass spectrometer. ### Claim 75 (depends on 74) The system of claim 74, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 76 A method of controlling a mass spectrometer in a Multiple Reaction Monitoring (MRM) analysis of a compound, the method performed by a programmed controller of an automated mass analyzer and comprising: receiving from an input source signals representing an identifier identifying the compound comprising a plurality of substances; receiving at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each substance would be expected to be received from a LC column associated with the mass spectrometer; using the identifier, automatically accessing data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determining a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; providing the command signal set to the mass spectrometer, in order to configure the mass spectrometer to analyze the portion of the compound for a plurality of scan cycles by applying one or more voltages to the mass spectrometer; and adjusting the command signal set applied to the mass spectrometer in at least one scan cycle of the plurality of scan cycles based on data generated by the mass spectrometer in an earlier scan cycle to at least one of: i) confirm one or more substances identified in the earlier scan cycle, and ii) correct for variations in elution time from the LC column. ### Claim 77 (depends on 76) The method of claim 76, wherein the command signal set is configured to adjust which individual selective scans are performed in each scan cycle based on the at least one designation identifying the specified time and the time range tolerance in which each of the plurality of substances would be expected to be received from the LC column. ### Claim 78 (depends on 76) The method of claim 76, wherein a duty cycle of each scan cycle is based on the at least one designation identifying the specified time and the time range tolerance in which each of the plurality of substances would be expected to be received from the LC column. ### Claim 79 (depends on 76) The method of claim 76, further comprising automatically determining an optimal duty cycle for each of the plurality of substances based on the at least one designation, wherein the command signal set is configured to cause the mass spectrometer to analyze the portion of the compound based on the optimal duty cycles. ### Claim 80 (depends on 76) The method of claim 76, wherein the command signal set is configured to operate the mass spectrometer such that, at each of a plurality of time points during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with at least one of the plurality of substances when the time point is within the respective time range tolerance identified for the at least one of the plurality of substances. ### Claim 81 (depends on 76) The method of claim 76, wherein the command signal set is configured to operate the mass spectrometer such that for each scan cycle during the MRM analysis, the mass spectrometer is configured to monitor for precursor ions and respective product ions associated with one or more selected substances of the plurality of substances when the scan cycle occurs within the respective time range tolerance identified for the one or more selected substances. ### Claim 82 (depends on 76) The method of claim 76, wherein the at least one designation identifying the specified time and the time range tolerance is received from at least one of an input device operated by a user and a data store communicatively coupled with the programmed controller. ### Claim 83 (depends on 76) The method of claim 76, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device. ### Claim 84 (depends on 76) The method of claim 76, wherein the identifier identifies parent-daughter transitions of interest. ### Claim 85 (depends on 76) The method of claim 76, wherein the identifier identifies toxins or drugs of abuse for screening of a biological sample. ### Claim 86 (depends on 76) The method of claim 76, wherein the identifier identifies pesticide residues for screening of a food, beverage, or environmental sample. ### Claim 87 (depends on 76) The method of claim 76, wherein the plurality of substances analyzed in the compound is greater than 100. ### Claim 88 A system for the automated MRM analysis of compounds, the system comprising: a mass spectrometer adapted to receive ions from an ion source, a controller adapted to: receive from an input source signals representing an identifier identifying a compound comprising a plurality of substances; receive at least one designation for each of the plurality of substances, wherein the at least one designation identifies a specified time and a time range tolerance in which each of the plurality of substances would be expected to be received from a LC column associated with the mass spectrometer; use the identifier to automatically access data comprising analysis parameters associated with the identifier and, using the accessed data, automatically determine a set of command signals for use by the mass spectrometer in analyzing at least a portion of the compound; and provide output signals representing the command signal set to the mass spectrometer, for use by the mass spectrometer in analyzing the portion of the compound for a plurality of scan cycles, wherein the command signal set is adjusted in at least one scan cycle of the plurality of scan cycles based on data generated by the mass spectrometer in an earlier scan cycle to at least one of: i) confirm one or more substances identified in the earlier scan cycle, and ii) correct for variations in elution time from the LC column. ### Claim 89 (depends on 88) The system of claim 88, wherein the command signal set controls one or more voltages applied to the mass spectrometer. ### Claim 90 (depends on 89) The system of claim 89, wherein the mass spectrometer comprises at least one of a triple quad mass spectrometer, QTrap, and QqTOF device.