Patent Application
20180033598
The teachings herein relate to high-field asymmetric waveform ion mass spectrometry (FAIMS) or differential mobility spectrometry (DMS). More particularly the teachings herein relate to systems and methods for quantitating lipids using a FAIMS or DMS device.
Lipids are naturally occurring organic molecules. They are generally characterized as being insoluble in water and soluble by organic solvents. Lipids are abundant in many different types of animal samples or matrices including, but not limited to, plasma, heart, liver, brain, muscle, whole blood, urine and cells. Lipids are also abundant in other types of samples or matrices including, but not limited to, milk, edible oils, and meat. Identifying and quantifying the lipids in an animal matrix can be useful in identifying and treating disease, for example. Identifying and quantifying the lipids in other matrices, such as food matrices, can be useful in verifying the integrity or safety of those matrices. Unfortunately, currently, there is no single system or method for identifying and quantifying all the lipids present in a particular matrix in a reasonable amount of time.
Tandem mass spectrometry is a method that is used to both identify and quantify or quantitate compounds or molecules in a sample matrix. In a tandem mass spectrometer, a precursor ion is selected in a mass filter, fragmented, and the product ions are analyzed in a mass analyzer. The entire process of selecting a precursor ion, fragmenting it, and analyzing the resulting product ions by mass-to-charge ratio (m/z) is referred to as tandem mass spectrometry, mass spectrometry/mass spectrometry (MS/MS), or an MS/MS scan. The product ion intensity or spectrum produced from MS/MS can be used to identify a compound (the precursor ion) in a sample, and the intensity of one or more product ions can be used to quantitate the amount of the compound present in the sample.
Information dependent analysis (IDA) is a flexible tandem mass spectrometry method in which a user can specify criteria for performing MS/MS while a sample is being introduced into the tandem mass spectrometer. For example, in an IDA method a precursor ion or mass spectrometry (MS) survey scan is performed to generate a precursor ion peak list. The user can select criteria to filter the peak list for a subset of the precursor ions on the peak list. MS/MS is then performed on each precursor ion of the subset of precursor ions. A product ion intensity or spectrum is produced for each precursor ion. MS/MS is repeatedly performed on the precursor ions of the subset of precursor ions as the sample is being introduced into the tandem mass spectrometer. The sample is introduced to the ion source of the tandem mass spectrometer through an injection or a chromatographic run, for example.
One type of MS/MS performed during an IDA method is referred to as multiple reaction monitoring (MRM), selected reaction monitoring (SRM), or as an MRM or SRM scan or transition. In an MRM scan, for example, a single precursor ion is selected and fragmented, a single product ion is then selected from the resulting product ions, and the selected product ion is mass analyzed. MRM is typically used for quantitative analysis. In other words, MRM is typically used to quantitate the amount of a precursor ion in a sample from the intensity of a production.
Some tandem mass spectrometers, such as AB SCIEX's QTRAP®, allow IDA methods to perform MRM. This is very useful for multi-analyte screening methods, including lipid analysis.
Unfortunately, however, even using MRM based tandem mass spectrometry methods it has been difficult to characterize all of the lipids in a particular type of matrix. Complete lipid characterization has been difficult because many matrices include large numbers of isobaric and near isobaric interferences that confound identification and accurate quantitation. In general, isobaric interference occurs when a sample contains another compound that has or produces a product ion with a similar m/z as the analyte, or compound of interest. In the case of lipids, many classes of lipids include lipids that interfere with the lipids of another class. This problem, coupled with complicated sample preparation techniques and data analysis needed for lipids, highlights the need for a complete solution that addresses these difficulties and provides a simplified method for analysis.
As a result, system and methods are need to identify and quantitate all the lipids present in a particular type of sample matrix with a reasonable amount of time.
Various embodiments of systems and methods are provided for quantitating known lipid molecules of a particular matrix using a differential mobility spectrometry (DMS) device during a targeted multiple reaction monitoring (MRM) acquisition experiment. Before the experiment, the known lipid molecules of the matrix are grouped into lipid classes and the lipid classes are further grouped into a pass-through group and a mobility separation group. The pass-through group includes lipid classes with lipid molecules known to produce isobaric interferences with other lipid molecules. The mobility separation group includes lipid classes with lipid molecules known to produce isobaric interferences.
An HPLC separation system introduces a matrix sample via infusion through low-carryover tubing. An ion source ionizes the matrix sample producing an ion beam. A DMS device receives an ion beam from the ion source for a first injection and a second injection of the matrix sample. For the first injection, the DMS device is put into passive mode and does not actively resolve lipid molecules. For the second injection, the DMS device is used to resolve isobaric interferences. In order to resolve isobaric interferences, the DMS device receives and applies different compensation voltages (CoV) values to the ion beam. The DMS device receives and applies CoV values stored for each of the lipid classes in the mobility separation group.
A tandem mass spectrometer receives a first ion beam from the DMS device for the first injection. The tandem mass spectrometer performs, for a first plurality of cycles, an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the pass-through group and stores a first set of intensity values of each MRM scan for the first plurality of cycles.
The tandem mass spectrometer receives a second ion beam that is separated according to ion mobility by the DMS device for the second injection. The tandem mass spectrometer performs, for a second plurality of cycles, an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the mobility separation group and stores a second set of intensity values of each MRM scan for the second plurality of cycles.
A processor in communication with the mass spectrometer and the DMS applies quantitates each lipid molecule in the matrix sample by comparing the first set of intensity values and the second set of intensity values to MRM intensity and concentration values for the known standards of the known lipid molecules of the matrix.
The skilled artisan will understand that the drawings, described below, are for illustration purposes only. The drawings are not intended to limit the scope of the present teachings in any way.
Before one or more embodiments of the present teachings are described in detail, one skilled in the art will appreciate that the present teachings are not limited in their application to the details of construction, the arrangements of components, and the arrangement of steps set forth in the following detailed description or illustrated in the drawings. Also, it is to be understood that the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting.
Computer system 100 may be coupled via bus 102 to a display 112, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 114, including alphanumeric and other keys, is coupled to bus 102 for communicating information and command selections to processor 104. Another type of user input device is cursor control 116, such as a mouse, a trackball or cursor direction keys for communicating direction information and command selections to processor 104 and for controlling cursor movement on display 112. This input device typically has two degrees of freedom in two axes, a first axis (i.e., x) and a second axis (i.e., y), that allows the device to specify positions in a plane.
A computer system 100 can perform the present teachings. Consistent with certain implementations of the present teachings, results are provided by computer system 100 in response to processor 104 executing one or more sequences of one or more instructions contained in memory 106. Such instructions may be read into memory 106 from another computer-readable medium, such as storage device 110. Execution of the sequences of instructions contained in memory 106 causes processor 104 to perform the process described herein. Alternatively hard-wired circuitry may be used in place of or in combination with software instructions to implement the present teachings. Thus implementations of the present teachings are not limited to any specific combination of hardware circuitry and software.
The term “computer-readable medium” as used herein refers to any media that participates in providing instructions to processor 104 for execution. Such a medium may take many forms, including but not limited to, non-volatile media, volatile media, and transmission media. Non-volatile media includes, for example, optical or magnetic disks, such as storage device 110. Volatile media includes dynamic memory, such as memory 106. Transmission media includes coaxial cables, copper wire, and fiber optics, including the wires that comprise bus 102.
Common forms of computer-readable media include, for example, a floppy disk, a flexible disk, hard disk, magnetic tape, or any other magnetic medium, a CD-ROM, digital video disc (DVD), a Blu-ray Disc, any other optical medium, a thumb drive, a memory card, a RAM, PROM, and EPROM, a FLASH-EPROM, any other memory chip or cartridge, or any other tangible medium from which a computer can read.
Various forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to processor 104 for execution. For example, the instructions may initially be carried on the magnetic disk of a remote computer. The remote computer can load the instructions into its dynamic memory and send the instructions over a telephone line using a modem. A modem local to computer system 100 can receive the data on the telephone line and use an infra-red transmitter to convert the data to an infra-red signal. An infra-red detector coupled to bus 102 can receive the data carried in the infra-red signal and place the data on bus 102. Bus 102 carries the data to memory 106, from which processor 104 retrieves and executes the instructions. The instructions received by memory 106 may optionally be stored on storage device 110 either before or after execution by processor 104.
In accordance with various embodiments, instructions configured to be executed by a processor to perform a method are stored on a computer-readable medium. The computer-readable medium can be a device that stores digital information. For example, a computer-readable medium includes a compact disc read-only memory (CD-ROM) as is known in the art for storing software. The computer-readable medium is accessed by a processor suitable for executing instructions configured to be executed.
The following descriptions of various implementations of the present teachings have been presented for purposes of illustration and description. It is not exhaustive and does not limit the present teachings to the precise form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practicing of the present teachings. Additionally, the described implementation includes software but the present teachings may be implemented as a combination of hardware and software or in hardware alone. The present teachings may be implemented with both object-oriented and non-object-oriented programming systems.
As described above, a major challenge in lipid analysis is the many isobaric and near isobaric interferences present in highly complex samples that confound identification and accurate quantitation. This problem, coupled with complicated sample preparation techniques and data analysis, highlights the need for a complete solution that addresses these difficulties and provides a simplified method for analysis.
In various embodiments, a novel lipidomics platform is developed that includes simplified sample preparation, automated methods, and streamlined data processing techniques that enables facile, quantitative lipid analysis. Differential mobility spectrometry (DMS) has been shown to be able to resolve isobaric interferences.
For IDA methods, differential mobility spectrometry (DMS) has been shown to be able to resolve isobaric interferences. Specifically, SCIEX's SelexION™ ion mobility technology has been utilized to enhance the quality of m/z analysis by pre-separating ions of similar m/z, thereby removing these isobaric interferences.
Unlike traditional ion mobility, ions 250 are not separated in time as they traverse the device. Instead, ions 250 are separated in trajectory based on the difference in their mobility between the high field and low field portions of applied RF voltage source 230. The high field is applied between plate 210 and plate 220 for a short period of time, and then a low field is applied in the opposite direction for a longer period of time. Any difference between the low-field and high-field mobility of an ion of a compound of interest causes it to migrate towards one of the plates. The ion is steered back towards the center-line of the device by the application of a second voltage offset, known as the CoV of DC voltage source 240, a compound-specific parameter that can be used to selectively filter out all other ions. Rapid switching of the CoV allows the user to concurrently monitor many different compounds. Ions 270 selected by the combination of SV and CoV, leave DMS device 200 through opening 280 to the remainder of the mass spectrometer (not shown). DMS device 200 is located between an ion source (not shown) and the remainder of the mass spectrometer, for example.
In general, DMS device 200 has two modes of operation. In the first mode, DMS device 200 is on, SV and CoV voltages are applied, and ions are separated. This is, for example, the enabled mode.
In the second mode of operation, DMS device 200 is off, the SV is set to zero and ions 250 are simply transported from opening 260 to opening 280. This is, for example, the disabled or transparent mode of DMS device 200.
In the enabled mode, DMS device 200 can acquire data for a single MRM transition in 25 milliseconds (ms), for example, including an inter-scan pause time of 20 ms. In transparent mode, the delay through DMS device 200 is negligible.
In various embodiments, a DMS device is used for targeted profiling of hundreds of lipid species from 10 different lipid classes allowing for comprehensive coverage.
Serum samples were analyzed quantitatively using a unique internal standard labeling protocol, a novel selectivity tool (DMS) and novel lipid data analysis software. Applying a kit for simplified sample extraction and preparation, a serum matrix is used following the protocols provided. An LC-DMS-QTRAP® System is used, for example, for targeted profiling of hundreds of lipid species from 10 different lipid classes, allowing for comprehensive coverage. This system allows for: 1. quantitative results for each lipid class as a sum of individual species; 2. mole percent composition, obtained computationally from lipid molecular species data; and 3. accurate lipid species compositions. The data is compared with historical data generated by alternative methods. Samples are quantitated using software accompanying the full solution, which incorporates the novel labeled internal standards available as a kit, developed for this platform.
Quantitative lipid species measurements are obtained from the following complex lipid classes: diacylglycerols (DAGs), triacylglycerols (TAGs), phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), sphingomyelins (SMs), lysophosphatidylcholines (LPCs) and lysophosphatidylethanolamines (LPEs), free fatty acids (FFAs), cholesteryl esters (CEs) and ceramides (CERs). Covering these classes requires a multi-injection approach but data can be collected in short, fast gradients up 5 minutes run time per injection (for three injections). The three injections classes cover TAGs and SMs, CEs, CERs and DAGs and FFAs, PE/PCs and their lyso components (LPC/LPEs).
In order to be able to screen a particular matrix type for lipids, an MRM method is built for that particular matrix. The MRM method is built over time from experimental data, for example.
These 1200 different lipid species are grouped into lipid classes 320 based on similar chemical structure. The lipid classes for plasma can include, but are not limited to, phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysophosphatidylcholine (LPC), lysophosphatidylethanolamine (LPE), triacylglycerol (TAG), diacylglycerol (DAG), cholestryl esters (CE), free fatty acids (FFA), sphingomyelin (SM), ceramide (CER), hexosylceramide (HCer), lactosylceramide (LCer), and dihexosylceramide (DCer).
Each lipid class includes one or more lipids 330. Each lipid 330 is then identified and quantitated using one or more MRM transition 340. As described above, each MRM transition is a precursor ion mass-to-charge ratio (m/z) value and a product ion m/z value.
Also as described above, some lipids 330 may include MRM transition 340 precursor or product ion m/z values that are similar or the same as those of other lipids 330. This produces isobaric interferences. As a result, a DMS device is used to separate precursor ions during the analysis. A particular precursor ion is distinguished from other precursor ions by selecting a CoV DMS parameter value for the precursor ion. Since lipids of a particular class have a similar structure, a CoV value for a lipid class can be used to distinguish all the precursor ions of the class from lipids in other classes. In other words, a CoV value is experimentally determined for a lipid class.
Not all lipid classes 320, however, include lipids 330 that have isobaric interferences with lipids 330 of classes. As a result, it is first determined what lipids 330 of matrix 310 have isobaric interferences. Then it is determined which lipid classes 320 include a lipid with an isobaric interference. Finally, a CoV value is determined for the lipid classes that have lipids with an isobaric interference. In other words, lipid classes 320 are further grouped as interference or classes with a CoV value, or as non-interference classes or classes without a CoV value.
Essentially, groups 451 and 452 allow the MS/MS to be performed with and without the DMS turned on, respectively. By separately analyzing these groups, the total analysis time using the instrument is decreased. In other words, analyzing the lipid classes of group 452 with the DMS acting as a pass through device increases the overall analysis time.
In various embodiments, the analysis is further decreased by additionally ordering the lipid classes in group 451 according to the DMS CoV parameter value 460 of the lipid class. Because it takes time to change the CoV of the DMS and this time is dependent on the amount of the change, if the lipid classes are ordered according to increasing or decreasing CoV values, the data acquisition time can be reduced.
Separation device 510 is configured to sequentially receive a first injection and a second injection of matrix sample 560. Separation device 510 is also configured to separate known lipid molecules of the matrix from the first injection and a second injection over time. Separation device 510 is, for example, a high performance liquid chromatography (HPLC) device. In various alternative embodiments, separation device 510 can perform one of a variety of separation techniques that include, but are not limited to, gas chromatography (GC), capillary electrophoresis (CE), or flow injection analysis (FIA).
In various embodiments, separation device 510 receives the first injection and the second injection through low-carryover tubing. Lipid molecules are sticking substances that easily adhere to surfaces. Low-carryover tubing prevents lipid molecules from adhering to tubing surfaces. One exemplary type of low-carryover tubing is PEEKsil™.
Before the experiment, the known lipid molecules of the matrix are grouped into lipid classes and the lipid classes are further grouped into a pass-through group and a mobility separation group. The pass-through group includes lipid classes with lipid molecules known to produce isobaric interferences with other lipid molecules. The mobility separation group includes lipid classes with lipid molecules known to produce isobaric interferences.
In various embodiments, lipid classes of the mobility separation group are further ordered according to increasing or decreasing CoV value to decrease the time needed to change CoV values of the DMS device during analysis of the second beam of ions.
Ion source 520 is configured to receive separated lipid molecules from separation device 510 for the first injection and the second injection. Ion source 520 is also configured to ionize the separated lipid molecules for the first injection and the second injection.
DMS device 530 is configured to receive a first beam of ions of the separated lipid molecules for the first injection and pass the first beam through without ion mobility separation. DMS device 530 is also configured to receive a second beam of ions of the separated lipid molecules for the second injection and sequentially mobility separate the second beam. The second beam of ions is sequentially separated by ion mobility according to CoV values experimentally predetermined for each lipid class of the mobility separation group. DMS device 530 can be a SelexION™ device, for example.
Tandem mass spectrometer 540 is configured to receive the first ion beam from the DMS device. Tandem mass spectrometer 540 is further configured to perform, for a first plurality of cycles, an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the pass-through group and store a first set of intensity values of each MRM scan for the first plurality of cycles.
Tandem mass spectrometer 540 is also configured to receive the second mobility separated ion beam from the DMS device. Tandem mass spectrometer 540 is further configured to perform, for a second plurality of cycles, an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the mobility separation group and store a second set of intensity values of each MRM scan for the second plurality of cycles. Each MRM transition of each lipid molecules is experimentally predetermined, for example.
In various embodiments, the first set of intensity values and the second set of intensity values are stored on in a memory or data storage device. The data storage device can be a storage device of tandem mass spectrometer 540 or a separate storage device.
Tandem mass spectrometer 540 can include one or more physical mass filters and one or more physical mass analyzers. A mass analyzer of tandem mass spectrometer 540 can include, but is not limited to, a time-of-flight (TOF), a quadrupole, an ion trap, a linear ion trap, an orbitrap, or a Fourier transform mass analyzer.
In various embodiments, tandem mass spectrometer 540 further performs each MRM scan for each lipid molecule of the known lipid molecules of the matrix using a predetermined polarity for each lipid class.
Processor 550 is in communication with tandem mass spectrometer 540 and DMS device 530, for example. Processor 550 is configured or programmed to receive the first set of intensity values and the second set of intensity values, to receive MRM intensity and concentration values for known standards of the known lipid molecules of the matrix, and to quantitate each lipid molecule in matrix sample 560. Processor 550 quantitates each lipid molecule in matrix sample 560 by comparing the first set of intensity values and the second set of intensity values to the MRM intensity and concentration values for the known standards of the known lipid molecules of the matrix. For example, average intensities values are calculated for each MRM of each lipid molecule over the first plurality of cycles or the second plurality of cycles. The average intensities values are then compared to the MRM intensity and concentration values for the known standards of the known lipid molecules of the matrix.
In various embodiments, processor 550 receives the first set of intensity values, the second set of intensity values, and the MRM intensity and concentration values for known standards of the known lipid molecules of the matrix from a memory or data storage device. The data storage device can be a storage device of tandem mass spectrometer 540, a storage device of processor 550, or a separate storage device.
Processor 560 can be, but is not limited to, the system of
In various embodiments, the quantitation is designed to accommodate differences in ionization efficiency of lipids classes as well as the differential fragmentation efficiency of lipids containing fatty acyl chains with different numbers of carbons and double bonds. Each lipid class has multiple internal standards that vary in chain length and degree of unsaturation, and have minimum or no interference with MRMs of target lipids. Target molecules are normalized by using the appropriate internal standard with the respective number of carbons and double bonds.
In various embodiments, a matrix for which lipid classes are experimentally predetermined can be an animal matrix. An animal matrix can include, but is not limited to, plasma, heart, liver, brain, muscle, whole blood, urine, or cells.
In various embodiments, a matrix for which lipid classes are experimentally predetermined can be a food matrix. A food matrix can include, but is not limited to, milk, edible oils, and meat.
In various embodiments, the lipid classes that the known lipid molecules of the matrix are grouped into include phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysophosphatidylcholine (LPC), lysophosphatidylethanolamine (LPE), triacylglycerol (TAG), diacylglycerol (DAG), cholestryl esters (CE), free fatty acids (FFA), sphingomyelin (SM), ceramide (CER), hexosylceramide (HCer), lactosylceramide (LCer), dihexosylceramide (DCer), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidic acid (PA), cardiolipin (CL), and oxidized fatty acid metabolites (eicosanoids).
In various embodiments, the matrix is plasma. The lipid classes that the known lipid molecules of plasma are grouped into include phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysophosphatidylcholine (LPC), lysophosphatidylethanolamine (LPE), triacylglycerol (TAG), diacylglycerol (DAG), cholestryl esters (CE), free fatty acids (FFA), sphingomyelin (SM), ceramide (CER), hexosylceramide (HCer), lactosylceramide (LCer), and dihexosylceramide (DCer).
In step 610 of the method of
In step 620, separated lipid molecules are received from the separation device for the first injection and the second injection and the separated lipid molecules are ionized for the first injection and the second injection using an ion source.
In step 630, a first beam of ions of the separated lipid molecules for the first injection is received and the first beam is passed through without ion mobility separation using a DMS device.
In step 640, a second beam of ions of the separated lipid molecules for the second injection is received and the second beam is sequentially mobility separated according to CoV values experimentally predetermined for each lipid class of the mobility separation group using the DMS device.
In step 650, the first ion beam is received from the DMS device, for a first plurality of cycles, an MRM scan is performed for at least one MRM transition for each lipid molecule of each lipid class of the pass-through group, and a first set of intensity values of each MRM scan for the first plurality of cycles is stored using a tandem mass spectrometer.
In step 660, the second mobility separated ion beam is received from the DMS device, for a second plurality of cycles, an MRM scan is performed for at least one MRM transition for each lipid molecule of each lipid class of the mobility separation group, and a second set of intensity values of each MRM scan for the second plurality of cycles is stored using the tandem mass spectrometer. Each MRM transition of each lipid molecules is experimentally predetermined; for example.
In step 670, the first set of intensity values and the second set of intensity values are received, MRM intensity and concentration values for known standards of the known lipid molecules of the matrix are received, and each lipid molecule in the matrix sample is quantitated using a processor. Each lipid molecule in the matrix sample is quantitated by comparing the first set of intensity values and the second set of intensity values to the MRM intensity and concentration values for the known standards of the known lipid molecules of the matrix.
While the present teachings are described in conjunction with various embodiments, it is not intended that the present teachings be limited to such embodiments. On the contrary, the present teachings encompass various alternatives, modifications, and equivalents, as will be appreciated by those of skill in the art.
Further, in describing various embodiments, the specification may have presented a method and/or process as a particular sequence of steps. However, to the extent that the method or process does not rely on the particular order of steps set forth herein, the method or process should not be limited to the particular sequence of steps described. As one of ordinary skill in the art would appreciate, other sequences of steps may be possible. Therefore, the particular order of the steps set forth in the specification should not be construed as limitations on the claims. In addition, the claims directed to the method and/or process should not be limited to the performance of their steps in the order written, and one skilled in the art can readily appreciate that the sequences may be varied and still remain within the spirit and scope of the various embodiments.
This application claims the benefit of U.S. Provisional Patent Application Ser. No. 62/113,290, filed Feb. 6, 2015, the content of which is incorporated by reference herein in its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/IB2016/050613 | 2/5/2016 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62113290 | Feb 2015 | US |
