1. A method for processing spectra, the method comprising: (a) obtaining a plurality of spectra, each spectrum in the plurality of spectra comprising a signal including a 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; (b) forming, with a computer, a signal cluster by clustering signals from the plurality of spectra with time-of-flights, mass-to-charge ratios, or values derived from time-of-flights or mass-to-charge ratios that are within a window that is defined using an expected signal width value; (c) determining a cluster center value associated with the signal cluster; and (d) creating an analytical model using the cluster center value, wherein the analytical model is capable of classifying samples into classes associated with different conditions, wherein the signal cluster is a first signal cluster, the window is a first cluster window, and the expected signal width is a first expected signal width, and wherein the method further includes forming a second signal cluster using a second cluster window, the second cluster window being defined using a second expected signal width.