Data Dependent MS/MS Analysis

A method of mass spectrometry comprising:

• generating a plurality of species of precursor ions;
• mass analysing the precursor ions so as to obtain first mass spectral data;
• varying the intensity profile of one or more species of precursor ions as a function of time so that different species of precursor ions are caused to have different intensity profiles as a function of time;
• performing a second mode of operation comprising subjecting precursor ions to reactions or fragmentation so as to produce product ions, and mass analysing the product ions so as to obtain second mass spectral data including intensity profiles that vary as a function of time;
• selecting a predetermined mass difference desired to be detected between a precursor ion in the first mass spectral data and a product ion in the second mass spectral data;
• comparing the first and second mass spectral data so as to identify a precursor ion in the first mass spectral data that has said predetermined mass difference to a product ion in the second mass spectral data;
• and
• determining whether said precursor ion is an ion of interest by determining if the intensity profile of said precursor ion matches the intensity profile of said product ion;
• wherein when a precursor ion is determined to be an ion of interest, said method further comprises a third mode in which said precursor ion of interest is isolated from other precursor ions, the isolated precursor ion is then fragmented or reacted so as to produce product ions, and the product ions are analysed so as to obtain product ion data.

A method of mass spectrometry comprising:

• using a separator to provide a plurality of separated precursor ions;
• passing the separated precursor ions into a fragmentation or reaction region and fragmenting or reacting the ions in a manner such that only some of the precursor ions fragment or react at any given time so as to result in both first precursor ions and first product ions;
• mass analysing the first precursor ions and first product ions so as to obtain mass spectral data;
• wherein the mass analysis comprises detecting the first precursor ions and first product ions, and recording an ion signal as a function of elution time of the separator;
• selecting a predetermined mass difference desired to be detected between a precursor ion in the mass spectral data and a product ion in the mass spectral data;
• comparing the mass spectral data so as to identify a precursor ion in the mass spectral data that has said predetermined mass difference to a product ion in the mass spectral data;
• and determining whether this precursor ion is an ion of interest by comparing the ion signal obtained for the identified precursor ion with the ion signal obtained for the product ion having the predetermined mass difference;
• wherein when a precursor ion is determined to be an ion of interest, said method further comprises a mode in which said precursor ion of interest is isolated from other precursor ions, the isolated precursor ion is then fragmented or reacted so as to produce product ions, and the product ions are analysed so as to obtain product ion data.

A method of mass spectrometry comprising:

• using a separator to provide a plurality of separated precursor ions;
• mass analysing the separated precursor ions in a first mode so as to obtain first mass spectral data;
• wherein the first mode comprises detecting precursor ions and recording an ion signal as a function of elution time of the separator;
• performing a second mode of operation comprising subjecting the separated precursor ions to reactions or fragmentation so as to produce product ions, and mass analysing the product ions so as to obtain second mass spectral data;
• wherein the second mode comprises detecting product ions and recording an ion signal as a function of elution time of the separator;
• determining if one or more predetermined product ion has been detected in the second mass spectral data;
• and
• determining whether a potential precursor ion of said predetermined product ion has been detected in said first mass spectral data by comparing the ion signal obtained in the first mode with the ion signal obtained in the second mode.

A mass spectrometer comprising:

• a separator for providing a plurality of separated precursor ions;
• a mass analyser;
• a reaction or fragmentation device;
• an ion filter;
• and
• a controller arranged and adapted to:
• mass analyse the separated precursor ions in the mass analyser in a first mode so as to obtain first mass spectral data;
• wherein the first mode comprises detecting precursor ions and recording an ion signal as a function of elution time of the separator;
• perform a second mode of operation comprising subjecting the separated precursor ions to reactions or fragmentation in the reaction or fragmentation device so as to produce product ions, and mass analysing the product ions in the mass analyser so as to obtain second mass spectral data;
• wherein the second mode comprises detecting product ions and recording an ion signal as a function of elution time of the separator;
• compare the first and second mass spectral data so as to identify a precursor ion in the first mass spectral data that has a pre-selected mass difference to a product ion in the second mass spectral data;
• and
• determine whether said precursor ion is a precursor ion of interest by comparing the ion signal obtained in the first mode with the ion signal obtained in the second mode;
• wherein the spectrometer is configured such that when a precursor ion is determined to be an ion of interest, a third mode of operation is performed in which said precursor ion of interest is isolated from other precursor ions by said ion filter, the isolated precursor ion is then fragmented or reacted in a fragmentation or reaction device so as to produce product ions, and the product ions are analysed in an ion analyser so as to obtain product ion data.

A mass spectrometer comprising:

• an ion source for generating a plurality of species of precursor ions;
• separation means for varying the intensity profile of one or more species of precursor ions as a function of time;
• a reaction of fragmentation device;
• an ion filter;
• and
• a mass analyser;
• wherein said mass spectrometer is arranged and adapted to:
• mass analyse the precursor ions in the mass analyser so as to obtain first mass spectral data in a first mode of operation, said separation means varying the intensity profile of one or more species of precursor ions as a function of time so that different species of precursor ions are caused to have different intensity profiles as a function of time;
• perform a second mode of operation comprising subjecting precursor ions to reactions or fragmentation in said reaction of fragmentation device so as to produce product ions, and mass analysing the product ions in the mass analyser so as to obtain second mass spectral data including intensity profiles that vary as a function of time;
• compare the first and second mass spectral data so as to identify a precursor ion in the first mass spectral data that has a pre-selected mass difference to a product ion in the second mass spectral data;
• and
• determine whether said precursor ion is a precursor ion of interest by determining if the intensity profile of said precursor ion matches the intensity profile of said product ion;
• wherein the spectrometer is configured such that when a precursor ion is determined to be an ion of interest, a third mode of operation is performed in which said precursor ion of interest is isolated from other precursor ions by said ion filter, the isolated precursor ion is then fragmented or reacted in a fragmentation or reaction device so as to produce product ions, and the product ions are analysed in an ion analyser so as to obtain product ion data.

A mass spectrometer comprising:

• a separator for providing a plurality of separated precursor ions;
• a mass analyser;
• a reaction or fragmentation device;
• an ion filter;
• and
• a controller arranged and adapted to:
• transmit separated precursor ions into the reaction or fragmentation device and react or fragment the ions in a manner such that only some of the precursor ions fragment or react at any given time so as to result in both first precursor ions and first product ions;
• mass analyse the first precursor ions and first product ions in the mass analyser so as to obtain mass spectral data;
• wherein the mass analyser is configured to detect the first precursor ions and first product ions, and record an ion signal as a function of elution time of the separator;
• compare the mass spectral data so as to identify a precursor ion in the mass spectral data that has a preselected mass difference to a product ion in the mass spectral data;
• and determine whether this precursor ion is an ion of interest by comparing the ion signal obtained for the identified precursor ion with the ion signal obtained for the product ion having the predetermined mass difference;
• wherein the spectrometer is configured such that when a precursor ion is determined to be an ion of interest, a further mode of operation is performed in which said precursor ion of interest is isolated from other precursor ions by said ion filter, the isolated precursor ion is then fragmented or reacted in a fragmentation or reaction device so as to produce product ions, and the product ions are analysed in an ion analyser so as to obtain product ion data.

A mass spectrometer comprising:

• a separator for providing a plurality of separated precursor ions;
• a mass analyser;
• a reaction or fragmentation device;
• and
• a controller arranged and adapted to:
• mass analyse separated precursor ions in the mass analyser in a first mode so as to obtain first mass spectral data;
• wherein the first mode comprises detecting precursor ions and recording an ion signal as a function of elution time of the separator;
• perform a second mode of operation comprising subjecting the separated precursor ions to reactions or fragmentation in the reaction or fragmentation device so as to produce product ions, and mass analysing the product ions in the mass analyser so as to obtain second mass spectral data;
• wherein the second mode comprises detecting product ions and recording an ion signal as a function of elution time of the separator;
• determine if one or more predetermined product ion has been detected in the second mass spectral data;
• and
• determine whether a potential precursor ion of said predetermined product ion has been detected in said first mass spectral data by comparing the ion signal obtained in the first mode with the ion signal obtained in the second mode.