Biopolymer sequences by MALDI granddaughter ion spectra

Method for the determination of terminal sequences of a protein using a tandem mass spectrometer, the method comprising:

• (a) acquiring granddaughter mass spectra of different species of in-source decay ISD fragment ion of the same fragmentation series, each granddaughter mass spectrum being acquired by
• (i) preparing the protein together with a matrix substance as a sample on a sample support;
• (ii) placing the sample support in the ion source;
• (iii) bombarding the sample on the sample support with light pulses from a pulsed laser with such a high energy density that it causes spontaneous fragmentations of a part of the protein whereby different species of ISD fragment ions are formed;
• (iv) accelerating the ions and injecting them into a first mass spectrometer of the tandem mass spectrometer;
• (v) selecting one species of the ISD fragment ions in the first mass spectrometer of the tandem mass spectrometer;
• (vi) fragmenting the selected ISD fragment ions at least partially to granddaughter ions by means of gas collisions (CID), surface collisions (SID) photon collisions (PID) or metastable decay (LID);
• and
• (vii) measuring the granddaughter ions in a second mass spectrometer of the tandem mass spectrometer to form a granddaughter mass spectrum;
• (b) comparing the granddaughter mass spectra to determine one fixed ion fragmentation series that is not shifted on all of the granddaughter mass spectra;
• and
• (c) using the mass differences of the fixed ion fragmentation series to read out the terminal sequence of the protein.