Method of correlating precursor and fragment ions using ion mobility and mass to charge ratio

A method of mass spectrometry comprising:

• separating precursor ions according to ion mobility by a Field Asymmetric Ion Mobility Separation (FAIMS) device;
• mass filtering precursor ions from a single separation cycle of the Field Asymmetric Ion Mobility Separation (FAIMS) device according to their mass to charge ratio with a mass filter, wherein the mass to charge ratios of the precursor ions transmitted by the mass filter vary with time;
• and
• repeatedly alternating between performing a first mode of operation and performing a second mode of operation on the ion mobility separated and mass filtered precursor ions from the single separation cycle of the Field Asymmetric Ion Mobility Separation (FAIMS) device;
• wherein performing the first mode of operation comprises:
• fragmenting or reacting the ion mobility separated and mass filtered precursor ions in a fragmentation or reaction device to form fragment or product ions;
• urging the fragment or product ions through the fragmentation or reaction device such that fragment or product ions derived from different precursor ions that have been separated according to their ion mobilities are maintained spatially separated from each other as they are urged through the fragmentation or reaction device;
• and
• detecting the fragment or product ions;
• and
• performing the second mode of operation comprises:
• the ion mobility separated and mass filtered precursor ions bypassing the fragmentation or reaction device, or being transmitted to the fragmentation or reaction device but being substantially not fragmented;
• maintaining the ion mobility separated and mass filtered precursor ions separated according to their ion mobilities as they bypass the fragmentation or reaction device or as they are transmitted through the fragmentation or reaction device;
• and
• detecting the ion mobility separated and mass filtered precursor ions;
• and
• the method further comprising:
• associating fragment or product ions detected when performing the first mode of operation to ion mobility separated and mass filtered precursor ions detected when performing the second mode of operation.

A mass spectrometer comprising:

• an ion mobility separator;
• a mass filter;
• fragmentation or reaction device;
• an ion detector or mass analyser;
• and
• a controller arranged and adapted to control the spectrometer to:
• separate precursor ions according to ion mobility in said ion mobility separator;
• mass filter precursor ions from a single separation cycle of the ion mobility separator according to their mass to charge ratio with said mass filter, wherein the mass to charge ratios of the precursor ions transmitted by the mass filter vary with time;
• and
• repeatedly alternate between operating in a first mode of operation and operating in a second mode of operation on the ion mobility separated and mass filtered precursor ions from the single separation cycle of the ion mobility separator;
• wherein operating the spectrometer in the first mode of operation comprises:
• fragmenting or reacting the ion mobility separated and mass filtered precursor ions in said fragmentation or reaction device to form fragment or product ions;
• urging the fragment or product ions through the fragmentation or reaction device such that fragment or product ions derived from different precursor ions that have been separated according to ion mobility are maintained spatially separated from each other as they are urged through the fragmentation or reaction device;
• and
• detecting the fragment or product ions;
• and
• operating the spectrometer in the second mode of operation comprises:
• the ion mobility separated and mass filtered precursor ions bypassing the fragmentation or reaction device, or being transmitted to the fragmentation or reaction device but being substantially not fragmented;
• maintaining the ion mobility separated and mass filtered precursor ions separated according to their ion mobilities as they bypass the fragmentation or reaction device or as they are transmitted through the fragmentation or reaction device;
• and
• detecting the ion mobility separated and mass filtered precursor ions with a detector or mass analyser;
• and
• the controller arranged and adapted to control the spectrometer to:
• associate fragment or product ions detected when operating in the first mode of operation to ion mobility separated and mass filtered precursor ions detected when operating in the second mode of operation.