Method for Extracting cIEF-MS Profiles from m/z versus Time Arrays

A method for separating intensity peaks from data collected in a separation device coupled mass spectrometry experiment, comprising:

• receiving a three dimensional (3-D) array of intensity measurements measured as a function of m/z and time from a separation device coupled mass spectrometer that separates one or more compounds from a sample over a time period and mass analyzes the one or more compounds at each time of a plurality of times of the time period using a processor;
• converting the 3-D array to an n×m intensity matrix D using the processor, wherein the n rows correspond to measured m/z values or values of a mass-related parameter calculated from the measured m/z values and the m columns correspond to the plurality of times or values of a time-related parameter calculated from the plurality of times, and
• applying nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix M and an intensity matrix A of the equation D=MA using the processor, wherein the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time-related parameter that separates the peak (i) from the 3-D array and the NMF is applied to produce in column (i) of the M matrix intensity values in terms of the measured m/z values or the values of the mass-related parameter corresponding to the peak (i).

A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor to perform a method for separating intensity peaks from data collected in a separation device coupled mass spectrometry experiment, the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a control module and an analysis module;
• instructing a separation device to separate one or more compounds from a sample over a time period using the control module;
• instructing an ion source to ionize the separated one or more compounds received from the separation device using the control module, producing an ion beam of one or more precursor ions;
• instructing a mass spectrometer to receive the ion beam from the ion source and mass analyze a mass range of the ion beam at each time of a plurality of times of the time period using the control module, producing a three dimensional (3-D) array of intensity measurements measured as a function of mass-to-charge ratio (m/z) and time for the time period;
• and
• receiving the 3-D array from the mass spectrometer using the analysis module;
• converting the 3-D array to an n×m intensity matrix D using the analysis module, wherein the n rows correspond to measured m/z values or values of a mass-related parameter calculated from the measured m/z values and the m columns correspond to the plurality of times or values of a time-related parameter calculated from the plurality of times;
• and
• applying nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix M and an intensity matrix A of the equation D=MA using the analysis module, wherein the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time-related parameter that separates the peak (i) from the 3-D array and the NMF is applied to produce in column (i) of the M matrix intensity values in terms of the measured m/z values or the values of the mass-related parameter corresponding to the peak (i).