Method and system for determining whether a drug will be effective on a patient with a disease
A process of determining whether a patient with a disease or disorder will be responsive to a drug, used to treat the disease or disorder, including obtaining a test spectrum produced by a mass spectrometer from a serum produced from the patient. The test spectrum may be processed to determine a relation to a group of class labeled spectra produced from respective serum from other patients having the or similar clinical stage same disease or disorder and known to have responded or not responded to the drug. Based on the relation of the test spectrum to the group of class labeled spectra, a determination may be made as to whether the patient will be responsive to the drug.
1 . A method of pre-processing a mass spectrum for subsequent classification of the mass spectrum using a training set, comprising the steps of:
a) subtracting background contained in the spectrum to produce a background subtracted spectrum, wherein the subtracting step comprises (i) estimating, in a moving window comprising a range of m/z values in said mass spectral data using robust asymmetric estimates, non-constant levels of background and (ii) subtracting the estimated background from the mass spectral data;
b) normalizing the background subtracted spectrum; and
c) aligning the normalized, background subtracted spectrum to a predefined mass scale.
2 . The method of claim 1 , wherein the mass spectrum is obtained from a blood-based sample of a human patient.
3 . The method of claim 1 , wherein the training set comprises class-labeled spectra of human patients.
4 . The method of claim 1 , wherein the step of normalizing the background subtracted spectrum comprises performing a partial ion current normalization.
5 . The method of claim 1 , wherein the step of normalizing the background subtracted spectrum comprises performing a total ion current normalization.
6 . The method of claim 1 , wherein the aligning step c) further comprises the step of aligning the normalized, background subtracted spectrum to a list of peak clusters identified from a group of mass spectra from blood-based samples which are both close in m/z position and well separated from each other in the m/z axis.
7 . The method of claim 6 , wherein the list of peak clusters are characterized by a center (m/z position) and a width (m/z range), and wherein one or more of the following m/z positions are within the list of peak clusters: 6434.50, 6632.18, 11686.94, 15131.14, 15871.47 and 28102.55.
8 . The method of claim 6 , wherein step c) further comprises the step of aligning the normalized, background subtracted spectrum to peak clusters centered at the following m/z positions: 6434.50, 6632.18, 11686.94, 15131.14, 15871.47 and 28102.55.