Method for analyzing mass spectra
A method that analyzes mass spectra using a digital computer is disclosed. The method includes entering into a digital computer a data set obtained from mass spectra from a plurality of samples. Each sample is, or is to be assigned to a class within a class set having two or more classes and each class is characterized by a different biological status. A classification model is then formed. The classification model discriminates between the classes in the class set.
1. A method for analyzing mass spectra, the method comprising:
detecting signals including signal intensifies in a plurality of spectra, wherein each spectrum in the plurality of spectra comprises data representing signal strength as a function of time-of-flight, mass-to-charge ratio, or a value derived from time-of-flight or mass-to-charge ratio;
forming at least one signal cluster by clustering signals with similar times-of-flight, mass-to-charge ratios, or values derived from times-of-flights or mass-to-charge ratios;
determining a predetermined number of signals, wherein the predetermined number of signals represents a minimum number of signals for a selected signal cluster;
selecting one or more signal clusters from the plurality of signal clusters if the number of signals in a signal cluster meets or exceeds the predetermined number of signals and excluding one or more signal clusters from the plurality of signal clusters if the number of signals in a signal cluster is below the predetermined number of signals; and
selecting the times-of-flights, the mass-to-charge ratios, or the values derived from the times-of-flights or the mass-to-charge ratios of the selected one or more signal clusters.
2. The method of claim 1 wherein the plurality of mass spectra is a first plurality of mass spectra and wherein the method further comprises:
forming a second plurality of mass spectra, wherein the second plurality of mass spectra is formed using the selected times-of flights, the mass-to-charge ratios, or the values derived from the selected times-of flights or mass-to-charge ratios.
3. The method of claim 2 further comprising normalizing signal intensity values in the second plurality of mass spectra.
4. The method of claim 2
wherein the plurality of mass spectra is from a plurality of samples, and wherein each sample is, or is to be assigned to a class within a class set comprising two or more classes, each class being characterized by a different biological status.
5. The method of claim 2 further comprising modifying the second plurality of mass spectra by adding estimates for missing signals.
6. The method of claim 1 wherein the plurality of spectra is generated using a surface enhanced laser desorption ionization process.
7. A computer readable medium comprising:
code for detecting signals including signal intensities in a plurality of spectra, wherein each spectrum in the plurality of spectra comprises data representing signal strength as a function of time-of-flight, mass-to-charge ratio, or a value derived from time-of-flight or mass-to-charge ratio;
code for forming at least one signal cluster by clustering signals with similar times-of-flights, mass-to-charge ratios, or values derived from times-of-flights or mass-to-charge ratios;
code for determining a redetermined number of signals, wherein the predetermined number of signals represents a minimum number of signals for a selected signal cluster;
code for selecting one or more signal clusters from the plurality of signal clusters of the number of signals in a signal cluster meets or exceeds the predetermined number of signals and excluding one or more signal clusters from the plurality of signal clusters if the number of signals in a signal cluster is below the predetermined number of signals; and
code for selecting the times-of-flights, the mass-to-charge ratios, or the values derived from the times-of-flights or the mass-to-charge ratios of the selected one or more signal clusters.
8. The computer readable medium of claim 7 wherein the plurality of mass spectra is a first plurality of mass spectra and wherein the computer readable medium further comprises:
code for forming a second plurality of mass spectra, wherein the second plurality of mass spectra is formed using the times-of-flights, the mass-to-charge ratios, or the values derived from the times-of-flights or mass-to-charge ratios obtained from the selected signal clusters.
9. The computer readable medium of claim 8 further comprising code for normalizing signal intensity values in the second plurality of mass spectra.
10. The computer readable medium of claim 8 further comprising code for modifying the second plurality of mass spectra by adding estimates for missing signals.
11. A system comprising:
a gas phase ion spectrometer;
a digital computer adapted to process data from the gas phase ion spectrometer; and
the computer readable medium of claim 7 in operative association with the digital computer.
12. The computer readable medium of claim 7 wherein the plurality of spectra is generated using a surface enhanced laser desorption ionization process.