Data Independent Acquisition of Product Ion Spectra and Reference Spectra Library Matching

Abstract

Systems and methods are disclosed for analyzing a sample using overlapping precursor isolation windows. A mass analyzer of a tandem mass spectrometer is instructed to select and fragment at least two overlapping precursor isolation windows across a precursor ion mass range of a sample using a processor. The tandem mass spectrometer includes a mass analyzer that allows overlapping precursor isolation windows across the mass range of the sample.

What is claimed is: 
     
         1 . A system for analyzing a sample using overlapping precursor isolation windows, comprising:
 a tandem mass spectrometer that includes a mass analyzer that allows overlapping precursor isolation windows across a mass range of a sample; and   a processor in communication with the tandem mass spectrometer that instructs the mass analyzer to select and fragment at least two overlapping precursor isolation windows across the precursor ion mass range of the sample.   
     
     
         2 . The system of  claim 1 , wherein the at least two overlapping precursor isolation windows are overlapped to ensure that all isotopic forms of a compound are present in at least one precursor isolation window. 
     
     
         3 . The system of  claim 1 , wherein the at least two overlapping precursor isolation windows are overlapped to ensure all precursor ions across the precursor ion mass range are selected. 
     
     
         4 . The system of  claim 1 , wherein each of the at least two overlapping precursor isolation windows has a width >10 amu. 
     
     
         5 . The system of  claim 1 , wherein the mass analyzer allows overlapping precursor isolation windows across a mass range of a sample by moving a single precursor isolation window in a step wise manner across the mass range with precursor isolation window overlap between steps, producing consecutive overlapping precursor isolation windows. 
     
     
         6 . The system of  claim 5 , wherein the precursor isolation window overlap of the consecutive overlapping precursor isolation windows is reduced to a minimum value experimentally determined to match a fragment ion transmission profile achievable by the mass analyzer. 
     
     
         7 . The system of  claim 6 , wherein the precursor isolation window overlap of the consecutive overlapping precursor isolation windows is reduced to the minimum value to maintain a minimal size for the single precursor isolation window, a minimal number of consecutive overlapping precursor isolation windows to cover the mass range of the sample, and a minimal dwell time between cyclic acquisitions of the mass range of the sample. 
     
     
         8 . A method for analyzing a sample using overlapping precursor isolation windows, comprising:
 instructing a mass analyzer of a tandem mass spectrometer to select and fragment at least two overlapping precursor isolation windows across a precursor ion mass range of a sample using a processor, wherein the tandem mass spectrometer includes a mass analyzer that allows overlapping precursor isolation windows across the mass range of the sample.   
     
     
         9 . The method of  claim 8 , wherein the at least two overlapping precursor isolation windows are overlapped to ensure that all isotopic forms of a compound are present in at least one precursor isolation window. 
     
     
         10 . The method of  claim 8 , wherein the at least two overlapping precursor isolation windows are overlapped to ensure all precursor ions across the precursor ion mass range are selected. 
     
     
         11 . The method of  claim 8 , wherein each of the at least two overlapping precursor isolation windows has a width >10 amu. 
     
     
         12 . The method of  claim 8 , wherein the mass analyzer selects and fragments at least two overlapping precursor isolation windows across the precursor ion mass range of a sample by moving a single precursor isolation window in a step wise manner across the mass range with precursor isolation window overlap between steps, producing consecutive overlapping precursor isolation windows. 
     
     
         13 . The method of  claim 12 , wherein the precursor isolation window overlap of the consecutive overlapping precursor isolation windows is reduced to a minimum value experimentally determined to match a fragment ion transmission profile achievable by the mass analyzer. 
     
     
         14 . The method of  claim 13 , the precursor isolation window overlap of the consecutive overlapping precursor isolation windows is reduced to the minimum value to maintain a minimal size for the single precursor isolation window, a minimal number of consecutive overlapping precursor isolation windows to cover the mass range of the sample, and a minimal dwell time between cyclic acquisitions of the mass range of the sample. 
     
     
         15 . A computer program product, comprising a non-transitory tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for analyzing a sample using overlapping precursor isolation windows, the method comprising:
 providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a measurement module; and   instructing a mass analyzer of a tandem mass spectrometer to select and fragment at least two overlapping precursor isolation windows across a precursor ion mass range of a sample using measurement module, wherein the tandem mass spectrometer includes a mass analyzer that allows overlapping precursor isolation windows across the mass range of the sample.   
     
     
         16 . The computer program product of  claim 15 , wherein the at least two overlapping precursor isolation windows are overlapped to ensure that all isotopic forms of a compound are present in at least one precursor isolation window. 
     
     
         17 . The computer program product of  claim 15 , wherein the at least two overlapping precursor isolation windows are overlapped to ensure all precursor ions across the precursor ion mass range are selected. 
     
     
         18 . The computer program product of  claim 15 , wherein each of the at least two overlapping precursor isolation windows has a width >10 amu. 
     
     
         19 . The computer program product of  claim 15 , wherein the mass analyzer selects and fragments at least two overlapping precursor isolation windows across the precursor ion mass range of a sample by moving a single precursor isolation window in a step wise manner across the mass range with precursor isolation window overlap between steps, producing consecutive overlapping precursor isolation windows. 
     
     
         20 . The computer program product of  claim 19 , wherein the precursor isolation window overlap of the consecutive overlapping precursor isolation windows is reduced to a minimum value experimentally determined to match a fragment ion transmission profile achievable by the mass analyzer.