Patent Description:
Atmospheric pressure Electron Capture Dissociation ("AP-ECD") mass spectrometers are known wherein analyte ions generated by an Electrospray ("ESI") ion source interact with photoelectrons. A UV lamp is arranged to emit UV photons which are absorbed by gas, causing the release of photoelectrons. Analyte ions interact with the photoelectrons causing the analyte ions to fragment at atmospheric pressure.

A problem with known AP-ECD mass spectrometers is that it is difficult to associate parent ions with their fragment ions. Alternative techniques tend to associate parent ions with their fragment ions by selecting a single type of parent ion at a given time and fragmenting this single parent ion to determine its fragment ions. Although this technique has a relatively low duty cycle, since other parent ions are discarded whilst the single parent ion is selected, it provides a relatively simple method of associating parent ions with their fragment ions. However, in AP-ECD techniques there is no means of selecting a specific parent ion for fragmentation because the parent ions are arranged in a high pressure region and so the conventional techniques for ion selection cannot be used. Furthermore, once the analyte ions have been fragmented there is no known means of associating the fragment ions to their precursor ions. When a sample being analysed contains a mixture of analytes, this can result in complex fragment ion spectra which include photo-ionised solvent background peaks, dopant ions and their derivatives, un-reacted parent ions, as well as mixtures of fragment ions and charge-reduced species from different parent ions. Accordingly, assigning parent ions to their fragment ions remains a complex problem in AP-ECD techniques and this complexity limits the analytical utility and commercial acceptance of the technique.

<CIT> discloses techniques for performing retention-time matching of precursor and product ions and for constructing precursor and product ion spectra.

<NPL> discloses liquid chromatography-atmospheric pressure electron capture dissociation mass spectrometry for the structural analysis of peptides and proteins.

It is desired to provide an improved mass spectrometer and method of mass spectrometry. Preferably, it is desired to provide a mass spectrometer and method of mass spectrometry that are able to fragment parent ions via ECD or ETD at atmospheric pressure and then associate the resulting fragment ions with their parent ions.

From a first aspect the present invention provides a method of mass spectrometry as claimed in claim <NUM>.

The ECD and/or ETD reactions are preferably performed substantially at atmospheric pressure, although it is contemplated that the reactions could less preferably be performed at sub-atmospheric pressure.

In step (ii), the parent ions are preferably substantially only fragmented by ECD and/or ETD reactions.

The method preferably continuously and repeatedly performs said cycle.

A fragment ion produced by step (iii) is preferably associated with a parent ion when that fragment ion is mass analysed in the same cycle or in an immediately preceding or immediately subsequent cycle to the parent ion.

The step of subjecting parent ions to ECD and/or ETD preferably comprises causing said electrons and/or reagent anions to interact with parent ions within an RF ion guide or ion trap.

The present invention also provides a method of identifying an analyte, preferably a biomolecule, comprising ionising the analyte to form parent ions and further comprising the method described above.

The present invention also provides a mass spectrometer as claimed in claim <NUM>.

The mass spectrometers disclosed herein may further comprise:.

The mass spectrometer may further comprise either:.

According to an embodiment the mass spectrometer further comprises a device arranged and adapted to supply an AC or RF voltage to the electrodes. The AC or RF voltage preferably has an amplitude selected from the group consisting of: (i) < <NUM> V peak to peak; (ii) <NUM>-<NUM> V peak to peak; (iii) <NUM>-<NUM> V peak to peak; (iv) <NUM>-<NUM> V peak to peak; (v) <NUM>-<NUM> V peak to peak; (vi) <NUM>-<NUM> V peak to peak; (vii) <NUM>-<NUM> V peak to peak; (viii) <NUM>-<NUM> V peak to peak; (ix) <NUM>-<NUM> V peak to peak; (x) <NUM>-<NUM> V peak to peak; and (xi) > <NUM> V peak to peak.

The AC or RF voltage preferably has a frequency selected from the group consisting of: (i) < <NUM>; (ii) <NUM>-<NUM>; (iii) <NUM>-<NUM>; (iv) <NUM>-<NUM>; (v) <NUM>-<NUM>; (vi) <NUM>-<NUM>. <NUM>; (vii) <NUM>. <NUM>-<NUM>. <NUM>; (viii) <NUM>. <NUM>-<NUM>; (ix) <NUM>-<NUM>; (x) <NUM>-<NUM>; (xi) <NUM>-<NUM>; (xii) <NUM>-<NUM>; (xiii) <NUM>-<NUM>; (xiv) <NUM>-<NUM>; (xv) <NUM>-<NUM>; (xvi) <NUM>-<NUM>; (xvii) <NUM>-<NUM>; (xviii) <NUM>-<NUM>; (xix) <NUM>-<NUM>; (xx) <NUM>-<NUM>; (xxi) <NUM>-<NUM>; (xxii) <NUM>-<NUM>; (xxiii) <NUM>-<NUM>; (xxiv) <NUM>-<NUM>; and (xxv) > <NUM>.

The preferred embodiment addresses the problem of not being able to associate parent ions with fragment ions formed in an AP-ECD source. According to a preferred embodiment, parent ions are generated from a sample eluting from a liquid chromatography column. Reagent ions and/or electrons are then provided to the parent ions so as to subject the parent ions to ETD and/or ECD fragmentation via ion-ion or ion-electron reactions. For example, electrons may be generated by a UV lamp for causing the ECD reactions and the parent ions may be intermittently and repeatedly subjected to ECD conditions by switching the UV lamp ON and OFF. The electrons provide ECD reaction conditions and cause some parent ions to fragment and also generate intermediate product ions that are essentially undissociated parent ions of reduced charge (i.e. ECnoD ions). The parent ions and the fragment or product ions arrive alternately at the mass analyser and are mass analysed. Data processing is then used to associate the parent ions with their fragment or product ions, preferably based on their simultaneous liquid chromatographic elution time profiles. It is also be desirable to identify or obtain information from the intermediate product ions by causing them to fragment and correlating the fragment ions to their parent ions or intermediate product ions. The intermediate ions are intermittently fragmented by collisionally induced dissociation ("CID") so that intermediate ions and their fragment ions arrive alternately at the mass analyser. The intermediate product ions and their fragment ions are alternately mass analysed and data processing is then used to associate the CID fragment ions with their intermediate product ions or corresponding parent ions, preferably based on their simultaneous liquid chromatography elution time profiles.

According to the preferred embodiment, ECD is preferably the sole or dominant mechanism by which parent ions are caused to fragment or dissociate. However, other embodiments are also contemplated wherein the fragmentation process may also be assisted by ETD, in which analyte ions exchange charge with reagent ions. Less preferred embodiments are also contemplated wherein ETD may be the sole or dominant mechanism by which parent ions are caused to fragment or dissociate.

Various embodiments of the present invention will now be described, by way of example only, and with reference to the accompanying drawings, in which:.

<FIG> shows a schematic of a preferred embodiment in which parent ions and their fragment ions are essentially associated based on their liquid chromatography elution times. The basic components of this embodiment comprise a liquid chromatography device <NUM>, an ion source <NUM>, an ECD device <NUM>, a CID device <NUM> and a mass analyser <NUM>.

Different analytes elute from the liquid chromatography device <NUM> at different times and are then ionised by the ion source <NUM> so as to form parent ions. The parent ions then pass through an atmospheric pressure ECD device <NUM>. The ECD device <NUM> comprises a UV lamp that is repeatedly switched ON and OFF. When the lamp is OFF, the parent ions are not subjected to ECD conditions and so the parent ions simply continue to the mass analyser <NUM> and are then mass analysed. In contrast, when the UV lamp is switched ON, the UV lamp emits UV photons that are absorbed by a gas, resulting in the release of photoelectrons. These photoelectrons interact with the parent ions to produce ECD fragment and product ions. The product ions include ECnoD product ions, which are parent ions that have been reduced in charge due to the ECD conditions, but which have not dissociated. These fragment and product ions then pass to the mass analyser <NUM> and are mass analysed. As the UV lamp is repeatedly switched ON and OFF, the parent ions are intermittently and repeatedly subjected to ECD conditions such that the ions leaving the ECD device <NUM> alternate between parent ions and their corresponding fragment or product ions.

It will be appreciated that the liquid chromatography device <NUM> and the ion source <NUM> serve to generate parent ions that are spatially separated as they travel towards the ECD device <NUM> and mass analyser <NUM>. The UV lamp is switched ON and OFF at a rate that is sufficiently high that ions of each type of parent ion pass through the ECD device <NUM> during a time period in which the lamp is ON and also during a time period in which the lamp is OFF. The mass analyser <NUM> therefore detects a parent ion and its fragment or product ions at substantially the same time, i.e. at substantially the same liquid chromatography elution time. The parent ions and their respective fragment or product ions can therefore be associated with each other relatively easily and based on the fact they have been detected at substantially the same time.

As described above, subjecting the parent ions to ECD conditions produces intermediate ions such as ECnoD product ions. These ions may be charge reduced parent ions that have not dissociated under the ECD conditions; it is desirable to fragment these ECnoD product ions and detect their fragments in order to identify the ECnoD product ions and hence help to identify the analyte from which they are derived. It may therefore also be desirable to associate the ECnoD product ions with their respective fragment ions in order to do this.

As has been described above, the ECD device <NUM> subjects parent ions to ECD conditions so as to produce ECnoD product ions, which are then received at the CID device <NUM>. During a period in which the ECD conditions are present, the CID device <NUM> is initially inactive (i.e. operated in a low collision mode) such that the ECnoD product ions are not dissociated by CID and are detected by the mass analyser <NUM>. Whilst the ECD conditions are still present, the CID device <NUM> is then activated (i.e. operated in a high collision mode) such that the ECnoD product ions are subjected to coilisionally induced dissociation and consequently fragment into fragment ions. The CID fragments of the ECnoD product ions are then detected at the mass analyser <NUM>. As described above, the UV lamp is switched ON and OFF at a rate that is sufficiently high that parent ions of each type pass through the ECD device during a time period in which the lamp is ON and also during a time period in which the lamp is OFF. As the CID device <NUM> is inactive and then active within each period that the lamp is ON, the switching of the CID device <NUM> between its two modes occurs at a relatively high rate and so the mass analyser <NUM> will detect ECnoD product ions and their CID fragment ions at substantially the same time, i.e. at substantially the same liquid chromatography elution time. Corresponding parent ions will also be detected at substantially the same time, when the lamp is switched OFF. The CID fragment ions can therefore be associated with their ECnoD product ions and/or their parent ions relatively easily and based on the fact they have been detected at substantially the same time.

According to a preferred method, three scans may be performed. A first scan may be performed wherein the UV lamp is switched OFF so that no ECD fragment or product ions are generated and wherein the parent ions are not subjected to CID fragmentation. Parent ions are detected by the mass analyser <NUM> in this scan. A second scan may also be performed wherein the UV lamp is switched ON so that ECD fragment and ECnoD product ions are generated, but wherein the ECD fragment and product ions are not subjected to CID fragmentation. In this scan the mass analyser <NUM> detects the ECD fragment and product ions. A third scan may also be performed wherein the UV lamp is switched ON so that ECD fragment and ECnoD product ions are generated and wherein the resulting ECD fragment and product ions are then subjected to CID fragmentation. In this scan the mass analyser <NUM> detects the ECD fragment ions and CID fragment ions. The time profiles of the first and second scans may then be matched so as to match ECD fragment and product ions with their corresponding parent or precursor ions. The time profiles of the second and third scans may be used for matching ECnoD product ions with their corresponding CID fragment ions. The time profiles of the first and third scans may be used for matching the CID fragment ions to their parent ions. The three scans are preferably performed successively in a cycle and may be performed in any order in the cycle, although it is preferred that the second and third scans are performed one after the other. The cycle of the three scans is repeated continuously during the analysis of the analyte and at a rate that is sufficiently high to correlate the ions in the respective scans of each cycle.

<FIG> shows a schematic of a preferred embodiment in which parent ions and their fragment ions are essentially associated based on their ion mobility drift times. The basic components of this embodiment comprise an ion source <NUM>, an ion mobility spectrometer <NUM> (IMS), an ECD device <NUM>, a CID device <NUM> and a mass analyser <NUM>.

Parent ions are generated by the ion source <NUM> and then pass to the IMS device <NUM>. Different parent ions have different mobilities and hence pass through the IMS device <NUM> with different drift times. The different parent ions leave the IMS device <NUM> at different times and then pass through an atmospheric pressure ECD device <NUM>. The ECD device <NUM> operates as described above with regard to <FIG>. When the lamp is OFF, the parent ions are not subjected to ECD conditions and so the parent ions simply continue to the mass analyser <NUM> and are then mass analysed, in contrast, when the UV lamp is switched ON, the parent ions produce ECD fragment and product ions, including ECnoD product ions. These fragment and product ions then pass to the mass analyser <NUM> and are mass analysed. As the UV lamp is repeatedly switched ON and OFF, the parent ions are intermittently and repeatedly subjected to ECD conditions such that the ions leaving the ECD device <NUM> alternate between parent ions and their corresponding fragment or product ions.

It will be appreciated that the IMS device <NUM> spatially separates the parent ions as they travel towards the ECD device <NUM> and mass analyser <NUM>. The UV lamp is switched ON and OFF at a rate that is sufficiently high that ions of each type of parent ion pass through the ECD device during a time period in which the lamp is ON and also during a time period in which the lamp is OFF. The mass analyser <NUM> therefore detects a parent ion and its fragment or product ions at substantially the same time, i.e. at substantially the same IMS drift time. The parent ions and their respective fragment or product ions can therefore be associated with each other relatively easily and based on the fact that they have been detected at substantially the same time.

As described above, subjecting the parent ions to ECD conditions also produces intermediate ions such as ECnoD product ions. It is desirable to fragment these ECnoD product ions and detect their fragments in order to identify the ECnoD product ions and hence help to identify the anaiyte from which they are derived. It may therefore be desirable to associate the intermediate ions with their respective fragment ions in order to do this.

As has been described above, the ECD device <NUM> subjects parent ions to ECD conditions so as to produce ECnoD product ions, which are then received at the CID device <NUM>. During a period in which the ECD conditions are present, the CID device <NUM> is initially inactive (i.e. operated in a low collision mode) such that the ECnoD product ions are not dissociated by CID and are detected by the mass analyser <NUM>. Whilst the ECD conditions are still present, the CID device <NUM> is then activated (i.e. operated in a high collision mode) such that the ECnoD product ions are subjected to coilisionally induced dissociation and fragment into fragment ions. The CID fragments of the ECnoD product ions are then detected at the mass analyser <NUM>. As described above, the UV lamp is switched ON and OFF at a rate that is sufficiently high that parent ions of each type pass through the ECD device <NUM> during a time period in which the lamp is ON and also during a time period in which the lamp is OFF. As the CID device <NUM> is inactive and then active within each period that the lamp is ON, the switching of the CID device <NUM> between its two modes occurs at a relatively high rate and so the mass analyser <NUM> will detect ECnoD product ions and their CID fragment ions at substantially the same time, i.e. at substantially the same IMS drift time. Corresponding parent ions will also be detected at substantially the same time, when the lamp is switched OFF. The CID fragment ions can therefore be associated with their ECnoD product ions and/or parent ions relatively easily and based on the fact that they have been detected at substantially the same time. According to a preferred method, three scans may be performed, in a corresponding manner to that described above with respect to <FIG>.

The preferred embodiments enable parent ions and their and fragment or product ions to be associated with each other by matching similar liquid chromatography time profiles and/or ion mobility drift time profiles. The preferred methods are particularly advantageous and may be implemented in mass spectrometers fitted with an atmospheric pressure ECD fragmentation source. The preferred method differs substantially from conventional techniques in that conventional techniques select precursor or parent ions prior to an electron capture event and also do not match elution profiles. Furthermore, the technique of generating c- and z- type ions according to the preferred methods of the present invention is significantly simplified compared with existing vacuum ECD techniques that involve more complex and expensive instrumentation modifications.

The present invention is particularly beneficial for analysing and preferably identifying biomolecules. The present invention is particularly beneficial, in the preferred methods, for fragmenting and analysing disulphide linked biomolecules.

Although the specific embodiments have been described above in terms of an ECD device comprising a UV lamp, it is contemplated herein that other types of ECD devices may be used to generate ECD conditions in ways other than by using a UV lamp. For example, the ECD device may operate using a high voltage corona discharge, a glow discharge or a low temperature plasma. Furthermore, it is also contemplated that an ETD device may be used instead of an ECD device. It is also contemplated that rather than switching between activating and deactivating the ECD or ETD device, the parent ions may be switched between passing through and bypassing an ECD or ETD device that may be operating continuously.

It is also contemplated that a method of supplemental activation other than CID may be used to fragment the intermediate product ions, it is also contemplated that methods of supplemental activation may be performed under vacuum conditions rather than at atmospheric pressure.

In the specific embodiments described above, liquid chromatography and IMS techniques have been described for providing spatially separated parent ions to the ECD device. However, it will be appreciated that other separation means may be used to perform this function.

Claim 1:
A method of mass spectrometry comprising:
providing a plurality of different parent ions; and
performing at least one cycle comprising:
(i) mass analysing said parent ions so as to obtain first mass spectral data;
(ii) subjecting said parent ions to ECD and/or ETD to produce fragment and/or product ions; and mass analysing said fragment and/or product ions so as to obtain second mass spectral data;
(iii) subjecting said parent ions to ECD and/or ETD, thereby producing intermediate ions, wherein the intermediate ions are non-dissociated parent ions held together by non-covalent interactions and/or are charge-reduced parent ions that have not fragmented after being exposed to the ECD and/or ETD conditions; and subjecting said intermediate ions to a fragmentation technique other than ETD and/or ECD such that said intermediate ions fragment to form fragment ions, wherein said fragmentation technique other than ECD and/or ETD is Collisionally Induced Dissociation fragmentation; and mass analysing these fragment ions so as to obtain third mass spectral data; and
(iv) associating parent ions detected in said first mass spectral data with fragment and/or product ions detected in said second and/or third mass spectral data,
wherein the method alternates between steps (ii) and (iii) by passing the parent ions through a Collisionally Induced Dissociation fragmentation device that is repeatedly switched between a low collision mode to perform step (ii) and a high collision mode to perform step (iii).