Methods and apparatus for tandem mass spectrometry

A tandem mass spectrometer comprising an ionization source for ionizing a sample, a mass filter which receives ions from said ionization source, an ion fragmenter for producing daughter ions from parent ions exiting from said mass filter, a discontinuous output mass analyzer for mass analyzing ions produced by said fragmenter and a controller for setting said mass filter to transmit ions having mass-to-charge ratios within a predetermined range and for causing said discontinuous output mass spectrometer to produce a mass spectrum of the ions entering it, characterized in that said controller is programmed to:

• a) set said mass filter to transmit ions which have mass-to-charge ratios in a first predetermined range;
• b) determine from the output of said discontinuous mass analyzer whether any daughter ions of interest are comprised in the ions leaving said fragmenter while step a) is being carried out, and to flag said predetermined range if any are so detected;
• c) repeat steps a) and b) using different first predetermined ranges until said mass filter has been set to transmit all the mass-to-charge ratios which it is thought said parent ions may possess;
• d) set said mass filter to transmit ions which have mass-to-charge ratios in a second predetermined range which comprises one or more of the mass-to-charge ratios comprised in any one of said first predetermined ranges flagged in step b);
• e) cause said discontinuous output mass analyzer to record the mass spectrum of ions leaving said fragmenter while step d) is being carried out;
• f) repeat steps d) and e) using different said second predetermined ranges until said mass filter has been set to transmit all of the mass-to-charge ratios comprised in all of said first predetermined ranges flagged in step b).

A method of tandem mass spectrometry in which parent ions generated from a sample are passed through a mass filter and are fragmented into daughter ions and passed through a discontinuous output mass analyser, the method comprising the steps of:

• a) splitting a range of mass-to-charge ratios which it is though that parent ions of interest may possess into a plurality of smaller ranges,
• b) setting said mass filter to pass ions of each said smaller range in turn, and flagging the smaller ranges for which it is determined using said discontinuous output mass analyser that daughter ions of interest are produced;
• and
• c) setting said mass filter to pass each mass-to-charge ratio of said flagged ranges, and determining through said discontinuous output mass analyser the mass-to-charge ratios of fragmented ions produced for each of said mass-to-charge ratios passed.