Patent Publication Number: US-2019180993-A1

Title: System for performing manual segmentation of mass spectrometry data

Description:
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH 
     This invention was made with government support under federal grant number 1552240 from the NSF. The U.S. Government has certain rights to this invention. 
    
    
     FIELD OF THE INVENTION 
     Embodiments described herein relate to a system that performs segmentation of mass spectrometry data to improve the accuracy of data analysis. 
     SUMMARY OF THE INVENTION 
     The mass spectrometry segmentation system described herein assigns isotopic trace points to isotopic traces and assigns isotopic traces to isotopic envelopes using a probabilistic method. The system also accepts input from a user that manually segments mass spectrometry data presented to the user, updates assignment of isotopic trace points to isotopic traces and isotopic traces to isotopic envelopes, and stores the segmented data for further segmentation by a user or use in scientific analysis. 
     BACKGROUND 
     Mass spectrometry nomenclature may be ambiguous. For the purposes of this document, the following definitions will be used. First, isotopic trace refers accumulated signal of instances of a given molecule at a given charge state whose molecular formula contains the same isotopic composition, either in profile or centroided form. Second, isotopic envelope refers to the accumulated signal instances of a given molecule at a given charge state, including molecules with differing isotopic composition, either in profile or centroided form. Manual segmentation shall refer to the delineation of bounds of at least one isotopic trace or isotopic envelope by a human; that is, the isotopic trace point membership assessed by a human of as to being included in specific isotopic traces and which isotopic traces should be included in which isotopic envelopes for every usable point in a mass spectrometry run. Manual segmentation provides a means to collect all useable signals in a visualization of mass spectrometry data without the poor performance of automated computational segmentation. Manual segmentation without specialized software is possible but in most cases is done crudely using, for example, spreadsheet software. Some software allows three dimensional (3-D) viewing of mass spectrometry data, but does not allow a user to delineate signal bounds, accumulate signals into isotopic traces, accumulate isotopic traces into isotopic envelopes, or save said delineations or accumulations. 
     Mass spectrometry is a means of ascertaining the composition of a molecular sample. Existing means for generating a list of molecule types and quantities in a sample include the use of secondary or tandem mass spectrometry, also known as MS/MS coupled with data from the primary or MS1 mass spectrometry experimental component. The pairing of MS/MS information with MS1 information and the extraction of MS1 information are computational processes. MS1 information extraction provides the potential to accurately identify and quantify a greater portion of molecules in a sample by providing more discriminatory information and more accurate abundance measures than MS/MS means alone. 
     Automated computational means of extracting some isotopic traces or portions of isotopic envelopes from a file have been published. These methods do not capture the majority of signals in a sample, and have limited quantitative accuracy on the signals they do capture. One reason these methods perform so poorly is that the signal structure in a mass spectrometry file varies greatly, and algorithms that segment one type of signal well will typically segment other types of signal poorly. Manual segmentation—the delineation of bounds of at least one isotopic trace or isotopic envelope by a human—is a technique for which no software has been publicly released to date. 
     Manual segmentation provides a means to segment all useable signals in a mass spectrometry output without the poor performance of automated computational segmentation. Manual segmentation without specialized software is not possible in any but the crudest sense. Some software allows 3-d viewing of mass spectrometry data, but none allow a user to delineate signal bounds or save said delineations. 
     A method for segmenting mass spectrometry data is described herein, the method comprises retrieving, with an electronic processor, a plurality of isotopic trace points stored as mass spectrometry data in an electronic repository. The method includes identifying a plurality of isotopic traces, wherein of the plurality of isotopic traces comprises a subset of the plurality of isotopic trace points retrieved from the mass spectrometry data. The isotopic traces are identified as belonging to one of a plurality of isotopic envelopes. The method stores isotopic traces and isotopic envelopes identified as segmentation data, presenting, on an output device, the plurality of isotopic traces and isotopic envelopes to a user. The method accepts input from an input device segmenting the graphic display of mass spectrometry data, updating the mass spectrometry data and the segmentation data using the input segmenting the mass spectrometry data, and presenting, on the output device, an updated graphic display of the mass spectrometry data based on the user supplied input segmenting the mass spectrometry data. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  illustrates an example embodiment of the Manual Segmentation System. 
         FIG. 2  illustrates an example method for segmenting isotopic envelopes presented to a user on an output device. 
         FIG. 3  shows an example method for assigning isotopic points to isotopic traces and isotopic envelopes. 
         FIG. 4  shows an example method for assigning isotopic traces to isotopic envelopes. 
     
    
    
     DETAILED DESCRIPTION 
     One or more embodiments are described and illustrated in the following description and accompanying drawings. 
     In addition, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. For example, the use of “including,” “containing,” “comprising,” “having,” and variations thereof herein is meant to encompass the items listed thereafter and equivalents thereof as well as additional items. The terms “connected” and “coupled” are used broadly and encompass both direct and indirect connecting and coupling. Further, “connected” and “coupled” are not restricted to physical or mechanical connections or couplings and can include electrical connections or couplings, whether direct or indirect. Moreover, relational terms such as first and second, top and bottom, and the like may be used herein solely to distinguish one entity or action from another entity or action without necessarily requiring or implying any actual such relationship or order between such entities or actions. 
       FIG. 1  illustrates a block diagram of a system  100  for identifying and presenting isotopic traces and isotopic envelopes, and manually segmenting mass spectrometry data according to one embodiment. In the example embodiment shown in  FIG. 1 , the system  100  includes a user device  110 , a communication network  120 , and a server device  130 . The communication network  120  may be a wired or wireless communication network. Portions of the communication network  120  may be implemented using a wide area network, (for example, the Intranet), a local area network (for example, a Bluetooth™ network or Wi-Fi network), and combinations or derivatives thereof 
     The user device  120  may be a laptop or desktop computer or a server, although other devices, including a tablet computer or other portable computing device could also be utilized. The administrator device  110  includes an electronic processor  111 , a memory or a similar storage device  112 , an input device  113 , an output device  114 , and a communication interface  115 . The electronic processor  111 , the storage device  112 , an input device  113 , an output device  114 , and a communication interface  115  communicate over one or more communication lines or buses, wireless connections, or a combination thereof. It should be understood that, in various configurations, the user device  110  may include additional or alternative components than those illustrated in  FIG. 1  and may perform additional functions than the functionality described herein. For example, in some embodiments the user device  110  includes peripherals, for example, one or more output devices, for example, additional displays beyond output device  114 , a speaker (not shown), or the like, and one or more input devices, for example, a keypad, a touchscreen, a microphone, a camera, or the like (not shown). 
     The electronic processor  111  may include one or more microprocessors, application-specific integrated circuit (ASIC), or other suitable electronic devices. The storage device  112  includes a non-transitory, computer readable medium. As used in the present application, non-transitory computer-readable medium comprises all computer-readable media except for a transitory, propagating signal. Accordingly, the storage device  112  may include, for example, a hard disk, an optical storage device, a magnetic storage device, ROM (read only memory), RAM (random access memory), register memory, a processor cache, or a combination thereof 
     The communication interface  115  sends data to external devices or networks, receives data from external devices or networks, or a combination thereof. The communication interface  115  may include a transceiver for wirelessly communicating over communication network  120  and, optionally, one or more additional communication networks or connections. Additionally or alternatively, in some embodiments, the communication interface  115  includes a port for receiving a wire or cable, for example, an Ethernet cable or Universal Serial Bus (USB) cable to facilitate a connection to an external device or network. 
     The electronic processor  111  is electrically connected to and executes instructions stored in the storage device  112 . In particular, as illustrated in  FIG. 1 , the storage device  112  stores a segmentation data  116  storing data and information used by segmentation application software  117 . The segmentation application software  117 , interacting with operating system  118 , accesses mass spec data  119  to identify and present isotopic traces and isotopic envelopes. As described in more detail in  FIG. 2 , the user device  110 , through execution of the segmentation application software  117  by the electronic processor  111 , identifies isotopic traces and isotopic envelopes and presents both isotopic traces and isotopic envelopes on the output device  114 . When users interact with the presented isotopic traces and isotopic envelopes, the processor  111  may receive segmentation input from the input device  113  causing a change in the segmentation data  116 . 
     In some embodiments, a server device  130 , including a server processor  131 , a storage device  132 , an input device  133 , an output device  134 , and a communication interface  135  are included in system  100 . A request from user device  110  may be communicated over communication network  120  to server device  130 , causing server processor  131  to access the storage device  132  to retrieve all or part of mass spec data  136  stored on server  130 , which is then communicated to user device  110  over communication network  120 . It should be understood that mass spec data  119  and mass spec data  136  may store duplicate data, may store data but not be accessed by segmentation application software  117 , or store parts of the totality of mass spec data, or some combination of these data placements without impacting or restricting the operation of the embodiment of system  100 . 
     The system  100 , shown in  FIG. 1 , may also include one or more user devices executing the segmentation application software  117 , where the devices may be, for example, a personal computer, tablet computer, smart telephone, or similar device. It should be recognized that the segmentation data  116  and mass spec data  119  may be replicated and copies placed on a plurality of user devices  110  or server devices  130 . In some embodiments, the segmentation application software  117  may execute on the server device  130  and be viewed on the user device  110  using output device  114 . In still other embodiments, one or more users may access the segmentation data  116 , segmentation application software  117 , mass spec data  119  on the user device  110  communicating over the communication network  120 . 
       FIG. 1  illustrates only one example embodiment of the system  100 . The system  100  may include additional or fewer components in configurations different from the configuration illustrated in  FIG. 1 . For example, a plurality of storage devices, such as storage device  117  and storage device  132 , may store all or portions of segmentation data  116  and mass spec data  119  and may be communicated to the segmentation application software  117 , which may be on the user device  110  or server device  130 . Also, in some embodiments, the functionality described here as being performed by the server device  130  may be distributed over multiple servers or other electronic devices. 
       FIG. 2  illustrates example method  200  for segmenting isotopic envelopes presented to a user on an output device according to one embodiment. The segmentation application software  117  communicating through communication interface  115  with server device  130  retrieves mass spectrometry data  136  from storage device  132  or from mass spectrometry data  119  on user device  110 , or both (at block  205 ). The mass spectrometry data comprises isotopic trace points which may be measurements the mass-to-charge ratio of ions in tested matter. Such isotopic trace points are coupled to chromatographic techniques such as gas- or liquid chromatography which can be used to identify and characterize small molecules and proteins (proteomics). Mass spectrometry data typically contains a large number of isotopic trace points and requires that computers be used for data storage and processing. Determining which isotopic trace points should be placed in isotopic traces and which isotopic traces placed in which isotopic envelopes is difficult as many isotopic trace points can be placed in multiple isotopic traces, and many isotopic traces can potentially be placed in multiple isotopic envelopes, with the likelihood of erroneous placements at time high thus producing incorrect results. 
     In example embodiment shown in  FIG. 2 , method  200  retrieves mass spectrometry data (at block  205 ). The mass spectrometry data retrieved by segmentation application software  117  (at block  205 ) is identified, in this example embodiment, as a plurality of isotopic traces (at block  210 ) and a plurality of isotopic envelopers (at block  220 ). The plurality of isotopic envelopes comprises a plurality of isotopic traces, and isotopic envelopes comprises a plurality of isotopic trace points. The segmentation application software  117 , executing on electronic processor  111  in this example embodiment, identifies isotopic envelopes (at block  220 ) by placing isotopic trace points in isotopic traces, as described in further detail in  FIG. 3 , and placing isotopic traces into the most likely correct isotopic envelopes, as described in further detail in  FIG. 4 . 
     As shown in the example embodiment of  FIG. 2 , method  200  presents isotopic envelopes on output device  114  on user device  110  (at block  240 ). The segmentation application software  117  executing on electronic processor  111  presents isotopic envelopes as a plurality of isotopic trace points, a plurality of isotopic traces, and a plurality of isotopic envelopes in a graphical display on output device  114  wherein a user may review the plurality of isotopic trace points, isotopic traces, and isotopic envelopes. The segmentation application software accepts input from the user through input device  113  (at block  250 ) to segment the isotopic envelopes, isotopic traces, or isotopic trace points, or a combination of segmentation inputs. Segmentation input may include adding or removing isotopic trace points from isotopic traces, adding or removing isotopic traces from isotopic envelopes, or combining isotopic trace points into isotopic traces, combining isotopic traces into new isotopic envelopes, or a combination of these example segmentation inputs. While heuristic and mathematical methods may be used to determine isotopic traces and isotopic envelopes, many times users can visually determine more accurate isotopic envelopes and thus method  200  allows users provide segmentation input to manipulate mass spectrometry data. 
     The method  200  shown in the example embodiment of  FIG. 2  updates the mass spectrometry data  119 , the mass spectrometry data  136 , or both, and the segmentation data  116  (at block  260 ). The segmentation application software  117 , executing on electronic processor  111  in this example embodiment, uses segmentation input to update mass spectrometry data  119 , mass spectrometry data  136 , or both, and the segmentation data  116  in response to user input by adjusting the inclusion of isotopic trace points in isotopic traces, the inclusion of isotopic traces in isotopic envelopes, or both. The adjusted isotopic traces and isotopic envelopes are presented to the user on the output device  114  (at block  280 ). The user may continue to generate segmentation input from the input device, which is accepted by the segmentation application software  117  (at block  240 ) which updates mass spectrometry data  119 , the mass spectrometry data  136 , or both, and the segmentation data  116  (at block  260 ) and presented on the output device  114  (at block  280 ) until the user decides to stop providing segmentation input. 
       FIG. 3  shows an example method  210  for assigning isotopic points to isotopic traces. In this example embodiment, method  210  implemented by segmentation application software  117  executing on electronic processor  111  is applied when analyzing mass spectrometry data for display to a user, or after accepting user input ( FIG. 2 . at block  250 ), or both, but it should be understood that the example embodiment of method  210  could be used to assign isotopic trace points to isotopic traces prior to assigning a plurality of isotopic traces to isotopic envelopes. The segmentation application software  117  executing on electronic processor  111  may determine if any isotopic trace points remain unassigned to an isotopic trace (at decision block  211 ) and if unassigned isotopic trace points remain, identifies the highest intensity unsegmented isotopic trace point (at block  212 ). The most likely candidate isotopic trace for inclusion of the isotopic trace point is identified (at block  213 ) and if the probability that the highest intensity unsegmented point assignment be included in the most likely isotopic trace is greater than a user set threshold probability (at block  214 ), then the isotopic trace point is included in the highest probability isotopic trace (at block  215 ). Otherwise, the segmentation application software  117  executing on electronic processor  111  in this embodiment creates a new isotopic trace (at block  216 ) and adds the highest intensity unsegmented isotopic trace point to the new isotopic trace (at block  217 ) within the segmentation data  116 . The segmentation application software  117  determines if isotopic trace points remain unassigned to isotopic traces (at block  211 ) and if so, the segmentation application software  117  identifies the highest intensity unsegmented isotopic trace point (at block  212 ) and proceeds as described previously. If not, method  210  terminates. 
       FIG. 4 . shows further detail of an example embodiment of method  220  for assigning isotopic traces to isotopic envelopes. The segmentation application software  117  executing on electronic processor  111  calculates for a plurality of isotopic traces, a joint probability as a function of closeness, concurrence, and intensity relationship that an isotopic trace should be associated with at least one isotopic envelope. The isotopic trace with the highest probability of being assigned to an isotopic envelope, and the probability is greater than a threshold probability assigned set by the user, in this example embodiment, is assigned to the isotopic envelope. The segmentation application software  117  executing on electronic processor  111  determines if any isotopic traces remain unassigned to isotopic envelopes (at block  221 ) and if any isotopic traces remain unassigned calculates the intensity for the plurality of unassigned isotopic traces and identifies the highest intensity isotopic traces (at block  222 ). The segmentation application software  117  executing on electronic processor  111  determines the closeness of fit between the isotopic traces and at least one isotopic envelope (at block  223 ) using the mass number and the charge number (M/Z) distance of (1/n), where n is any whole integer. The segmentation application software  117  executing on electronic processor  111  determines the concurrence of emergence for the plurality of isotopic traces and at least one isotopic envelope (at block  224 ). The intensity relationship between the plurality of isotopic traces and at least one isotopic envelope is determined by segmentation application software  117  executing on electronic processor  111  (at block  225 ). In order to assign isotopic traces to isotopic envelopes, in this example embodiment, segmentation application software  117  executing on electronic processor  111  calculates the probability of a match between the plurality of isotopic traces and at least on isotopic envelope (at block  226 ) using the intensity, closeness of fit, concurrence, and intensity relationship. In this example embodiment, the segmentation application software  117  executing on electronic processor  111  determines if unassigned isotopic trace with the highest probability of being included in an isotopic envelope exceeds a user specified threshold probability (at block  227 ) and if so, assigns the unassigned isotopic trace to the associated isotopic envelope (at block  228 ). If the unassigned isotopic trace with the highest probability of being included in an isotopic envelope does not exceed the user specified threshold probability (at block  227 ) the segmentation application software  117  executing on electronic processor  111  assigns the unassigned isotopic trace to a new isotopic trace (at block  229 ). The segmentation application software  117  executing on electronic processor  111  determines if any unassigned isotopic traces remain, and if not, the assignment of isotopic traces to isotopic envelopes ends. 
     It should be recognized that in other, alternative embodiments, the segmentation application software  117  could execute on an application server, web server, or other computing device, without altering the functionality described here. In addition, the mass spec data, segmentation data, or both, could be located on a file server, web server, external storage device, or the like, again without altering the functionality of the segmentation application server  117  as described in this embodiment. 
     Various features and advantages of some embodiments are set forth in the following claims.