Patent ID: 8581179

Claim:
A method for sequence analysis of proteins by acquiring mass spectra of spontaneous, non-ergodic fragment ions (ISD ions) from a protein sample in a mass spectrometer that ionizes the sample by matrix assisted laser desorption and that has an ion detector with a secondary electron multiplier having an amplification, the method comprising: (a) preparing a matrix including the protein sample and a matrix substance that supports spontaneous, non-ergodic fragmentation; (b) initially adjusting the mass spectrometer so that only sample ions with masses at or above a mass range limit are analyzed, the mass range limit corresponding to a mass of the terminal amino acids of the proteins; (c) initially adjusting the amplification of the secondary electron multiplier so that a spontaneous, non-ergodic ISD fragment ion spectrum can be detected above chemical background noise for sample ions with masses at the mass range limit; (d) irradiating the matrix with UV laser pulses to produce sample ions, each pulse having a maximum duration of one nanosecond and being formed by a plurality of distinct spots, each spot having a diameter below one micrometer; (e) acquiring an individual time-of-flight mass spectrum from sample ions; (f) after step (e), increasing the amplification of the secondary electron multiplier; (g) after step (e), increasing the mass range limit; (h) repeating steps (d)-(g) for a predetermined number of times; and (i) adding-up the individual time-of-flight spectra to form a sum spectrum.