Patent Application
20080048109
The present invention relates generally to mass spectrometry, and more particularly to automated acquisition of MS/MS and MSn spectra utilizing data-dependent methodologies.
Data-dependent acquisition (also referred to, in various commercial implementations, as Information Dependent Acquisition (IDA), Data Directed Analysis (DDA), and AUTO MS/MS) is a valuable and widely-used tool in the mass spectrometry art, particularly for the analysis of complex samples. Generally described, data-dependent acquisition involves using data derived from an experimentally-acquired mass spectrum in an “on-the-fly” manner to direct the subsequent operation of a mass spectrometer; for example, a mass spectrometer may be switched between MS and MS/MS scan modes upon detection of an ion species of potential interest. Utilization of data-dependent acquisition methods in a mass spectrometer provides the ability to make automated, real-time decisions in order to maximize the useful information content of the acquired data, thereby avoiding or reducing the need to perform multiple chromatographic runs or injections of the analyte sample. These methods can be tailored for specific desired objectives, such as enhancing the number of peptide identifications from the analysis of a complex mixture of peptides derived from a biological sample.
Data-dependent acquisition methods may be characterized as having one or more input criteria, and one or more output actions. The input criteria employed for conventional data-dependent methods are generally based on parameters such as intensity, intensity pattern, mass window, mass difference (neutral loss), mass-to-charge (m/z) inclusion and exclusion lists, and product ion mass. The input criteria are employed to select one or more ion species that satisfy the criteria. The selected ion species are then subjected to an output action (examples of which include performing MS/MS or MSn analysis and/or high-resolution scanning). In one instance of a typical data-dependent experiment, a group of ions are mass analyzed, and ion species having mass spectral intensities exceeding a specified threshold are subsequently selected as precursor ions for MS/MS analysis, which may involve operations of isolation, dissociation of the precursor ions, and mass analysis of the product ions.
The growing use of mass spectrometry for the analysis of peptides, proteins, and other biomolecules has led researchers to develop new dissociation techniques, including pulsed-q dissociation (PQD) and electron transfer dissociation (ETD), that provide additional and/or different informational content relative to conventional techniques. However, the data-dependent acquisition methods described in the prior art have been largely limited to use with a single, conventional dissociation mode. While certain references in the prior art (see, e.g., LeBlanc et al., “Unique Scanning Capabilities of a New Hybrid Linear Ion Trap Mass Spectrometer (Q Trap) Used for High Sensitivity Proteomics Applications, Proteomics, vol. 3, pp. 859-869 (2003)) have described using data-dependent methods to automatically adjust dissociation parameters such as collision energy, there remains a need for novel data-dependent acquisition methods that can be employed with the recently developed advanced dissociation techniques to more fully exploit the opportunities for acquiring enhanced informational content.
Roughly described, a method of automated mass spectrometric analysis implemented in accordance with an embodiment of the present invention includes steps of acquiring a mass spectrum of ions derived from a sample, analyzing the mass spectrum to select an ion species of interest, selecting a dissociation type from a list of distinct candidate dissociation types by applying specified criteria based at least partially on a determined charge state of the ion species of interest, and dissociating the ion species using the selected dissociation type to produce product ions. Examples of candidate dissociation types include collisionally activated dissociation (CAD), pulsed-q dissociation (PQD), photodissociation, electron capture dissociation (ECD), electron transfer dissociation (ETD), and ETD followed by one or more stages of supplemental collisional activation or proton transfer reactions (PTR). An MS/MS spectrum of the product ions may then be acquired. This process may be repeated one or more times to produce higher-generation product ions and to acquire the corresponding MSn spectra.
In another embodiment of the invention, a mass spectrometer is provided that includes an ion source for generating ions from a sample to be analyzed, a mass analyzer for acquiring a mass spectrum of the ions, and at least one dissociation device. The mass analyzer and dissociation device(s) may be integrated into a common structure, such as a two-dimensional ion trap mass analyzer. The mass analyzer and each dissociation device communicate with a controller, which is programmed to select an ion species of interest from the mass spectrum and to select an appropriate dissociation type from a list of candidate dissociation types by applying specified criteria based at least partially on the determined charge state of the ion species of interest. The controller then directs the ion dissociation device to dissociate the ion species using the selected dissociation type to produce product ions.
By expanding the concept of data-dependent methodologies to include selection of dissociation type, embodiments of the present invention make more effective use of the capabilities of a mass spectrometer instrument and facilitate production of more useful data. In one simple example, it is known that certain dissociation techniques (e.g., ETD) are characterized by a strong dependence of dissociation efficiency on ion charge state, and thus may not yield meaningful results when applied to ions having a low charge state. In such a case, the mass spectrometer may be programmed to limit its use of the charge-state dependent dissociation technique to ion species having the requisite charge state, and to use an alternative dissociation technique, such as CAD, for ion species that do not meet the charge state criteria.
In the accompanying drawings:
As shown in
Mass analyzer 115 is in electronic communication with a controller 140, which includes hardware and/or software logic for performing the data analysis and control functions described below. Controller 140 may be implemented in any suitable form, such as one or a combination of specialized or general purpose processors, field-programmable gate arrays, and application-specific circuitry. In operation, controller 140 effects desired functions of mass spectrometer 100 (e.g., analytical scans, isolation, and dissociation) by adjusting voltages applied to the various electrodes of mass analyzer 115 by RF, DC and AC voltage sources 145, and also receives and processes signals from detectors 160 representative of mass spectra. As will be discussed in further detail below, controller 140 may be additionally configured to store and run data-dependent methods in which output actions are selected and executed in real time based on the application of input criteria to the acquired mass spectral data. The data-dependent methods, as well as the other control and data analysis functions, will typically be encoded in software or firmware instructions executed by controller 140.
In a preferred embodiment, the instrument operator defines the data-dependent methods by specifying (via, for example, a command script or a graphical user interface) the input criteria (as used herein, references to “criteria” are intended to include an instance where a single criterion is utilized), output action(s), and the relationship between the input criteria and the output action(s). In a simple example, the operator may define a data-dependent method in which MS/MS analysis is automatically performed on the three ion species exhibiting the greatest intensities in the MS spectrum. As discussed above, data-dependent methods of this type are known in the art. The present invention expands the capabilities of data-dependent methodology by including within its scope additional input criteria (e.g., charge state), additional output actions (e.g., multiple dissociation types) and more complex relationships between the input criteria and output actions. In one representative example, which will be discussed in further detail in connection with
In step 220, the mass spectrum is processed by controller 140 to select one or more ion species of interest by applying specified input criteria. According to the present example, controller 140 is programmed to select the three ion species yielding the highest intensities in the mass spectrum. Alternative implementations of this method may utilize other input criteria (including but not limited to those listed above) in place of or in combination with the intensity criteria.
In the next step 230, the charge state of the selected ion species is determined by analysis of the acquired mass spectrum. Various techniques are known in the art for the determination of ion charge state from the analysis of mass spectra. Examples of such techniques include the following:
1. If the mass spectrometric resolution is sufficiently high, the separation of the components of the isotopic cluster m/z peaks for a particular ion species allows determination of the charge state; thus, the separation in m/z units is ˜1/n (Dalton/unit charge), where n is the charge state. In certain cases, sufficiently high resolution may be obtained by performing one or more slow-speed scans (mass spectra) of limited mass range centered around the m/z value of the ion species of interest.
2. The observation of different cationized species of the same charge number and derived from the same neutral analyte may allow direct determination of the charge state; for example, sodium cations may replace protons in the formation of positive ions, yielding ions that are separated from the fully protonated analog by ˜22/n (Dalton/unit charge).
3. For proteins and other high molecular mass analytes, an ion series representative of a broad range of charge states is commonly observed. The charge state of a particular ion species may be derived from the measured m/z's of the ion species of interest and the adjacent member of the ion series.
4. Ions may be deliberately dissociated, either within the source or the mass analyzer/dissociation device, and the charge state determined by comparing the measured m/z values of the product ions with expected values.
5. The ions may be subjected to one or more stages of charge reduction via proton transfer or other charge-reducing reactions, and the charge state may be deduced by comparing the original mass spectrum with the mass spectrum of the charge-reduced ions.
The foregoing list is intended as illustrative rather than limiting, and those in the art will recognize that many other techniques are or may become available for determination of charge state. More accurate and reliable determination of charge state may be achieved by combining two or more of the foregoing techniques (or other charge state determination techniques). The selection of the appropriate charge state determination technique will be guided by considerations of the requisite accuracy/reliability of the determined charge state, the analyte type, the mass analyzer type, and computational expense (bearing in mind that multiple data-dependent acquisition cycles may need to be completed across a chromatographic elution peak of relatively short duration). In one implementation, the operator may specify or select a desired charge state determination technique from a list of available techniques prior to performing the analysis. It should be further noted that the charge state determination may be performed as part of the preprocessing operations discussed above, i.e., prior to or concurrently with selection of an ion species of interest.
As used herein, the term charge state may denote either a single value (e.g., +2) or a range of values (e.g., +2-4 or >+6). In certain implementations, it may not be necessary to determine the exact value of the charge state of the ion species of interest, but instead it may suffice, for the purposes of making the data-dependent decision, to assess whether the ion species of interest is either singly-charged or multiply-charged, or alternatively whether the ion species has a charge state that lies within one of a set of value ranges, e.g., +1, +2-3, +4-6, >+6. This determination can typically be conducted by application of a relatively simple, low computational cost algorithm.
It is further noted that certain charge state determination techniques require acquisition of only a single mass spectrum, whereas others rely on acquisition and processing of multiple mass spectra (e.g., enhanced-resolution scans or product ion spectra). Given the time constraint imposed by the duration of chromatographic elution, it is generally desirable to employ a charge state determination technique that provides acceptable accuracy and reliability while consuming as little time as possible in order to ensure that sufficient time is available to complete an adequate number of data-dependent acquisition cycles during the elution period.
Following determination of the charge state of the selected ion species, data system 140 uses the determined charge state to select the dissociation type in accordance with the specified relationship between the input criteria and output actions, step 240.
The foregoing examples are intended to illustrate how the invention may be implemented in a specific instance, and should not be construed as limiting the invention to any particular relationship between the determined ion species parameter and the selected dissociation type. The input criteria-dissociation type relationship employed for a given experiment will be formulated in view of various operational considerations and experimental objectives. The relationship may be simple (for example, switching between two dissociation types based solely on the charge state parameter), or may instead be highly complex, having several candidate dissociation types selectable according to a scheme based on multiple parameters, including but not limited to charge state, charge state density, m/z, mass, intensity, intensity pattern, neutral loss, product ion mass, m/z inclusion and exclusion lists, and structural information. For example, for a given precursor ion m/z, multiple MS/MS spectra may be acquired using different dissociation methods, For instance, +2 charge state peptide precursors having an m/z<600 will likely yield product ion spectra providing complementary information via both CAD and ETD followed by CAD.
In should be noted that in certain implementations, one possible data dependent output action is to refrain from any dissociation (and acquisition of an MS/MS spectrum) of a selected ion species, where such MS/MS spectrum is unlikely to yield meaningful information.
In step 250, an MS/MS or MSn spectrum is acquired for the selected ion species utilizing the dissociation type chosen in step 240. As is known in the art, acquisition of the MS/MS spectrum will typically involve refilling analyzer 115 with an ion population including the selected ion species and isolation of the selected ion species by applying a supplemental AC waveform that ejects all ions outside of the m/z range of interest, followed by resonant excitation of the selected ion species (for CAD or PQD), or mixing the ion species with reagent ions of opposite polarity (for ETD). The mass spectrum of the product ions may be generated by standard methods of mass-sequential ejection.
Per step 260, the charge state determination, dissociation type selection, and MS/MS spectrum acquisition steps are repeated for each of the selected ion species. Upon completion of this cycle, the method returns to step 210 for selection of a new set of ion species of interest.
While the foregoing embodiment has been described with reference to analyte cations (i.e., all analyte ions have been assigned positive charge states), it should be noted that the method and apparatus of the present invention is equally well-suited to analysis of analyte anions, wherein the list of candidate dissociation types may include negative electron transfer dissociation (NETD) and other techniques specially adapted for dissociation of analyte anions.
It will be recognized that the data-dependent methods described herein, whereby input criteria based at least partially on a determined charge state are applied to select a dissociation type, may be extended to other data-dependent output actions. For example, in a hybrid mass spectrometer having two distinct analyzer types (such as the LTQ Orbitrap mass spectrometer available from Thermo Fisher Scientific), charge state-based criteria may be applied to determine which one of the available analyzers is employed to produce a mass spectrum of ions derived from an ion species of interest (or, in another implementation, which dissociation device is utilized). Other output actions which may be selected by application of charge state based criteria include scan rate, analyzer mass range, and data processing algorithms.
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
This application claims the priority benefit under 35 U.S.C. §119(e) of U.S. provisional patent application No. 60/840,198 entitled “Data-Dependent Selection of Fragmentation Type” filed on Aug. 25, 2006, the disclosure of which is incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 60840198 | Aug 2006 | US |
