A method for diagnosing depression includes providing surface-enhanced laser desorption/ionization mass spectrometric (SELDI-MS) data of a plurality of proteins, said data obtained from a patient and comprising a plurality of peak values, and analyzing said peak values with an alternating decision tree comprising a set of tests of said data peaks values and associated prediction values, wherein said data is predictive of depression if a sum of the prediction values of said tree is greater than 1.0.