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1. 20 Undo REdO ZOOM 4 eto tea Et ND sut taie Deka Mtr IE Es veux Dus 20 Dui 21 Increase Decrease Vertical Zoom sees 21 Increase Decrease Horizontal Zoom essem 21 Spectrum VIEW sseseetetiesettitet textes EEE LEA E cau Ee RePEc taa E EIKIDen DEEG 21 Spectrum Thumbnail eese eter tda e ein ka nh er ats ron de SERE dia ii 22 Select Region orne EM 22 4 11 Export Spectrum Image oc ccccsccccccccavcccessnccrsecsenecseceacceddscnsctancsanccdeccanceacen 23 4 12 Copy Spectrum Image to Clipboard seseee 24 CHENOMX NMR SUITE USER MANUAL 4 13 Display Options sssini oiiaee aoa Ea an a ait 24 4 14 Preferences eee E E E E E A 25 5 PrOCESSON seoir noanoa ripara A A AAE ILE 28 5 1 OVEIVIEW rrean ia E AE E E E etl E 28 5 2 Quick Reference Guide sees nne nennen nnne nennen ne nnn nennen 29 5 3 Information To0ls inte e iene TIRE ge en aE 30 CSI EQUIP e 31 PH Editoreen eae UU UEM HMM I EE E DE eee 32 Spectrum Detalls PR 34 Processing History Sidebar cccceeeeeeee cece eeeeeeeaeesaeesa esse E E 34 S Processing LO0IS wis svcd ceteaiadanicedenace nidndchacicdneanesisndenddudevancadiadendcsteennmaie es 35 IJiERADAM T 36 Baseline Correction isossa naaa aiaa aaa a R daanenencaeedies 37 Line Broadening eere te Eie E E vere eres 38 Reference Deconvolution
2. File Menu a Open Ctrl O Cmd O Open Recent GJ Close Ctrl W Cmd W H Save Ctrl S Cmd S Save As a m Export Spectrum Image ass E Spectrum Details zs amp Send to Profiler Ctrl J Cmd J Preferences Exit m Edit Menu V Undo Ctrl Z Cmd Z 34 Redo Ctrl Y Cmd Y m Copy Spectrum Image to Clipboard View Menu X Scale eee Y Scale lol Zoom Show Entire Spectrum Ctrl Minus Cmd Minus Zoom Undo Zoom x Zoom Redo Zoom a Zoom Set Zoom Ctrl M Cmd M IP Zoom gt Select Region Ctrl T Cmd T y Zoom Auto Zoom Ctrl F Cmd F Te Zoom gt Increase Vertical Zoom Zoom gt Decrease Vertical Zoom e Zoom Increase Horizontal Zoom 2 is 5 2 Quick Reference Guide 29 CHENOMX NMR SUITE USER MANUAL Enom Linux Windows Mac OS X e Zoom Decrease Horizontal Zoom Edit Mode CSI Edit Mode pH m n Sidebar gt Legend Ctrl Shift L Cmd Shift L Y5 Sidebar Processing History Ctrl Shift H Cmd Shift H Show Sidebar Ctrl Shift S Cmd Shift S Show Spectrum Thumbnail Ctrl Shift T Cmd Shift T Processing Menu po Phasing Ctrl Alt 1 Cmd Alt 1 ace Baseline Correction Ctrl Alt 2 Cmd Alt 2 18 Line Broadening Ctrl Alt 3 Cmd Alt 3 AD Advanced gt Reference Deconvolution Ctrl Alt 4 Cmd Alt 4 iw Advanced gt Water Deletion Ctrl Alt 5 Cmd Alt 5 ase Advanced gt Reverse Spectrum C
3. Click Request License File to create a new e mail message in your system s default e mail client requesting activation of Chenomx NMR Suite Enter your name in the generated message and send the message If you do not have access to e mail call Chenomx at 1 780 432 0033 You will receive a license file cnxlic from a support staff member Save the license file to a folder on your computer Open any module of Chenomx NMR Suite The Chenomx Software Activation dialog appears again Click the Install License File button Browse to the folder in which you saved the license file select the file and click the Open button You have now activated Chenomx NMR Suite Click the Accept button to run the module that you selected If you have not purchased Chenomx NMR Suite or if you have not yet received your license file you can still use the software in evaluation mode When evaluating Chenomx NMR Suite you have complete access to every module with the following exceptions Saving profiled cnx files using Send to Processor exporting profiled data and performing spectral binning in Profiler Note that you can still process and save cnx files in Processor Using Send to Profiler in Processor Saving xcpd files in Compound Builder 1 2 Activation and Licensing 2 evomx CHENOMX NMR SUITE USER MANUAL To evaluate Chenomx NMR Suite 1 Open any module of Chenomx NMR Suite the Chenomx Software Activation d
4. Double click on a J modifier to change its coupling constant and coupling status including which spin definition the current one is coupled to if any e Only the Spin Definition Tabs for the currently selected spin system are visible at any given time e The tabs for spin definitions that are coupled to the currently selected one appear highlighted in bold in the Simulation view Related Topics e Spin Systems on page 70 e Spin Definitions on page 71 7 4 Information Tools 75 CHENOMX NMR SUITE USER MANUAL e J Modifiers on page 73 Simulation Details The bottom center pane in the Spin Simulator window displays simulation details information about the current simulation Simulation details include the simulation frequency numbers of spin systems and spin definitions spins and numbers of transitions present in the current simulation Tips and Tricks e When you do not have a spectrum overlay you can change the simulation frequency in the simulation details to explore the effects of spectrometer frequency on your simulated compound e When you overlay a spectrum the simulation frequency is set to match that of the spectrum overlay Related Topics e Spectrum Overlays on page 19 e Spin Systems on page 70 e Spin Definitions on page 71 7 4 Information Tools 76 Chapter 8 Compound Builder The Compound Builder module lets you create compound signatures so that you can identify an
5. You now have SDO and SD1 for the methyl groups 3 protons each at 0 978 and 1 031 ppm and SD2 and SD3 for the methine groups 1 proton each at 2 264 and 3 604 ppm with a tab for each spin definition in the Simulation view 5 Zoominto the two methyl signals near 1 0 ppm You can click and drag across the two corresponding entries in the Spin Navigator to provide a useful zoom level 6 Measurethe distance between the pairs of peaks in each doublet using the tape measure The right hand doublet measures about 7 02 Hz while the left hand one measures about 7 07 Hz 7 Select SDO 0 978 ppm by clicking on it in the graph or clicking on its tab in the Simulation view 8 Right click on SDO blue and click Add J Modifier 9 Enter aJ value of 7 02 Hz select Uncoupled Split with a split count of 1 and click OK 10 5 Spin Simulator 123 evomx CHENOMX NMR SUITE USER MANUAL 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Adjust first spin definition blue to fit the spectrum black You can adjust freely by clicking and dragging the peak shape or use eitherthe controls on the horizontal and vertical axis or the up down left and right arrow keys to restrict your adjustment to specific dimensions and directions Adjustthe width ofthe doublet using the controls to either side ofthe spin definition so that it better matches the spectrum A width of about 1 2
6. 7 1 Overview 1s Proline xss File Edit View Simulation Tools Pee oa Sa Simulation aeeie ele oec O Spin Definition 0 Protons 1 J Modifiers CoupledtoSDi 1 x 13 23 Hz CoupledtosD2 1x 7 57 Hz CoupledtoSD3 1 x 6 65 Hz coutedto sos 1 x 7 44 Hz Coupled to SDS 1 x 7 40 Hz Add Edit Delete Spin Definitions auae ss zs Zi E SD2 gt 7 57 Hz Center ppm 1 97844 mp e i Width sw 1 2974 Spin Definition 0 V Center 1 97844 ppm AL oo TEREK Frequency MHz Number of Spin Systems Number of Transitions Number of J Modifiers Simulation Details 799 81 1 116 of 116 possible amp 3 Bo LL pH 6 93 1 978 ppm 0 289 si Sidebar View Buttons Let you change the currently visible Sidebar view Simulation Sidebar view that displays Spin Definition Tabs for the currently selected spin system Also lets you select spin systems via a drop down menu and spin definitions via the tabs J Value Editor Lets you vary the J value for the currently selected J modifier 7 1 Overview 67 evomx CHENOMX NMR SUITE USER MANUAL J Modifier List Lets you add select edit or remove J modifiers associated with the currently selected spin definition Simulation Details Display information about the current simulation includ
7. Compound Details on page 91 8 3 Building Tools 89 Enom CHENOMX NMR SUITE USER MANUAL Manage Cluster IDs How do I change the order of cluster IDs in a signature Menu Location Icon s Tools Manage Cluster IDs 1 2 3 On the Tools menu click Manage Cluster IDs Click and drag the clusters in the list to change their order Or Select a cluster in the list and use the green up and down arrows to change the position ofthe cluster in the list Click OK Tips and Tricks Cluster IDs are used by the pH sensitivities dialog to determine which clusters should be considered as corresponding to the same signal across all of your selected data points Make sure that the clusters appear in the proper order in each of your data points before applying pH sensitivities A cluster that appears upfield from another cluster at one pH may appear downfield from the same cluster at a different pH Consider overlaying all of your data point spectra cnx in Processor or Profiler to better determine the behavior of clusters across the full pH range If you have used the signature to profile spectra changing the cluster IDs may make your existing fits of the compound invalid Related Topics pH Sensitivities on page 88 Cluster Navigator The Cluster Navigator lets you quickly move among the clusters that you have created in the current compound signature It appears in the top left corner of
8. The remaining spin definitions are quite complicated There is a lot of coupling among them including some to spin definitions that you have already fit Some of these links to solved spin definitions can help reduce the complexity of modeling the spin definitions that remain Start with SD3 since it is the last one that is well isolated from other signals Due to the complexity of this signal it is not immediately clear which measurements you can use to extract coupling constants However one clue exists in the geminal relationship between the protons responsible for this signal and SD2 You observed a coupling constant of 11 58 Hz previously between geminal protons so start by looking for a measurement of similar magnitude Measuring from an outermost peak to a peak near 11 58 Hz gives about 8 7 or 13 7 Hz The former value does not appear quite large enough for a geminal coupling so use the latter to couple SD3 to SD2 18 Adda J modifier to SD3 and couple it to SD2 using a New Split with a J value of 13 7 Hz SD3 should also be coupled to SD6 based on the original assignments There are two J modifiers available to create this link with J values of 8 79 and 6 52 Hz However based on the structure you can estimate the dihedral angle between these two protons as larger than that between SD2 and SD6 A larger dihedral angle implies a larger coupling constant according to the vicinal Karplus correlation so use the larger of the two her
9. For more direct control over the baseline correction applied to your spectrum you can specify endpoints linear fit or breakpoints cubic spline fit manually How do I apply baseline correction to my spectrum Menu Location Processing gt Baseline Correction 1 Switch to Baseline Correction mode HOUR Bc 2 Automatic Linear Click the Auto Linear button to automatically determine a Ctrl Alt 2 linear baseline adjustment Hotkey s Cmd Alt 2 Or Automatic Spline Click the Auto Spline button to automatically determine a set of breakpoints for a cubic spline based baseline adjustment 3 Manual Click on the spectrum to set breakpoints for a cubic spline fit Click and drag existing breakpoints including the endpoints to move them Hold down Control or Command to place breakpoints anywhere in the spectrum instead of directly on the spectrum line itself Hold down Shift while clicking on an existing breakpoint to delete it 4 Clickthe Accept button to apply your changes or click the Cancel button to discard them 5 4 Processing Tools 37 CHENOMX NMR SUITE USER MANUAL Tips and Tricks e Only apply baseline correction after you are satisfied with the phasing in your spectrum e Evenifyou intend to manually adjust baseline correction you may find it helpful to usethe Auto Linear function first Auto Linear lets Processor firstlocate the natural endpoints of the spectrum giving you a useful starting point
10. iac iixe ct iessnuececdstecndssbeeecsestanendescaecnuencdes 39 Eug E 40 Reverse Spectrim c ens ectes cesses sees tectus oninia ninii eren da xu ies tiaa 41 5 5 Importing and Exporting Data ssesseseeseee menm 41 Bosque uc 41 Send to Prohiler x diet t leva is Sedeeacanwees a SI UE 42 6 Profil OF e M ma 43 6 1 OVENVICW a EEUU 43 6 2 Quick Reference Guide eeeeseseeseeeeeeeen eene nennen nennen ne nnne nennen nn 44 6 3 Profiling Tools Lem net UE teta HIER p ou REN EE UI LE Pa Meu 46 Compound Table C M R 46 Custom Colors e EE PERPE Rem EI e Ee use d HERES 48 Pinned Compounds e iixtetcukenseee dx Ehe naea E eA EA uu acce RUN 49 Starred Compounds ettet E IPs RU Md eus 50 Quick Searches iriaren a iaweectostaesnathianscapiaensatiaeascaent 50 Goncentratlons eor rt etd E ween igen cee 52 Transforms REDE 53 Fit Automatically or E Peas eR RE MINE I IM EE 55 Enforce Transform Windows esseesseeeeem mmn 55 Maximum Concentrations cuiu ee cient eh ben LAE ERIT Eee XE EE AAEE 56 Scale Concentrations ote idxesticsi d axesdiun cedat ences dant coire EREA 57 Cluster Navigator eei edite iem Me Eee Yos e ue tds 58 6 4 Compound Set Tools n nis est nexis pu eins e icd Ea XE ddacewacend uA 59 Compound Sets Sidebar eU eet EORR Rer Ret Genres 59 Open Library Manager 2 citsccsdvesscaceedsenctdeaivacecetdatetivesrr
11. 1 2 Start the Export Spectrum Image wizard Choose a file format You can specify bitmap gif png or vector formats svg pdf eps Choose a folder and filename for the exported image Tips and Tricks If you plan to distribute the image via e mail or post it to a Web page use Portable Network Graphics png Graphics Interchange Format gif or Scalable Vector Graphics svg If you need an image that others can view or print on multiple computers use Portable Document Format pdf If you are preparing images for professional typesetting or publication use Encapsulated PostScript eps 4 11 Export Spectrum Image 23 CHENOMX NMR SUITE USER MANUAL Choose Do not shade area under lines to ensure that none of the peak shading effects are retained in the exported image Disabling shading can be useful when you export an image of an area containing many clusters as shading can create a very heavy look Related Topics e Spectrum View Tools on page 20 e Display Options on page 24 4 12 Copy Spectrum Image to Clipboard You can use Copy Spectrum Image to Clipboard to quickly make an image of the current Menu Location i Clipboard intermediary file Icon s m Tips and Tricks Edit Copy Spectrum Image to spectrum available to paste directly into another application without creating an e Theresolution ofthe spectrum image copied to the clipboard varies based
12. add an uncoupled J modifier to a spin definition 1 Selectthe spin definition to which you would like to add a J modifier 2 Openthe Add New J Modifier dialog 3 Enter a J value for the new J modifier in Hz 4 Select Uncoupled Split and specify a split count for the new J modifier 5 Click OK How do add a coupled J modifier to a spin definition 1 Selectone ofthe two spin definitions that you would like to link with a coupled J modifier 2 Openthe Add New J Modifier dialog 3 Enter aJ value for the new J modifier in Hz 7 3 Simulating Tools 73 CHENOMX NMR SUITE USER MANUAL Compound gt Edit Selected Menu tocarian J Modifier Icon s 4 Compound Delete Selected Menu Location P J Modifier Icon s Jy Menu Location Compound gt Uncouple Icon s e Compound Ungroup Selected Menu Locatii enu Location Splits Icon s J Compound gt Group Selected Menu Locatii enu Location Splits Icon s J 4 Select Coupled and select the spin definition to which you would like to link 5 Click OK How do edit an existing J modifier 1 Selecta spin definition Select a J modifier that you would like to edit Open the Edit Selected J Modifier dialog Make your desired changes Click OK u e w N How do I couple two spin definitions using splits that I have already defined 1 Select one of the two spin definitio
13. e Processing Tools on page 35 Send to Profiler When you finish processing a spectrum in Processor your nexttask is often to start profiling NEUESTE File Send to Profiler the spectrum in Profiler Send to Profiler closes the current spectrum in Processor and amp opens it in Profiler retaining any changes you have made in Processor Icon s Tips and Tricks Ctrl J Cmd J e Any changes that you have made to the spectrum in Processor are retained when you send the spectrum to Profiler and are visible if you bring the spectrum back into Processor However you still need to save the spectrum either in Processor or Profiler to permanently save those changes to the spectrum file Hotkey s Related Topics e Chapter 6 Profiler on page 43 5 5 Importing and Exporting Data 42 Chapter 6 Profiler The Profiler module helps you to identify and quantify compounds in a sample spectrum as wellas apply spectral analysis techniques like spectral binning You can fit any available compound to the current spectrum and you can modify the compounds displayed using compound sets and filters 6 1 Overview e occ eo File Edit View Compound Tools Help SN S4 vmn0B Legend a Serine Concentration 1185 2 uM 40 39 38 Number of Selected Clusters 1 lel Selection Center 3 97903 ppm 5 Profiler Lines s Spectrum Lin
14. e Remove Compound Sets on page 103 Rename Compound Sets You can rename Compound Sets or Smart Compound Sets after you have created them How do I rename a compound set LL le gt Rename Compound Set 1 Selecta compound set in the Compound Sets view Hon n 2 Click Rename Compound Set Ctrl R Hotkey s 3 Enteranew name for the set Cmd R 4 Press Enter Tips and Tricks e Click onthe name ofa selected compound set or right click on the name ofa compound set and select Rename to rename the set e You can rename a Smart Compound Set via the Edit Smart Compound Set dialog Related Topics e Compound Sets Sidebar on page 100 e Compound Sets on page 101 e Smart Compound Sets on page 102 Remove Compound Sets You can remove compound sets when you no longer need them 9 4 Compound Set Tools 103 CHENOMX NMR SUITE USER MANUAL How do I remove a compound set LL File gt Remove Compound Set 1 Selecta compound set in the Compound Sets view Icon s IF 2 Click Remove Compound Set Tips and Tricks e Right click on the name of a compound set and select Remove to remove the set Related Topics e Compound Sets Sidebar on page 100 e Compound Sets on page 101 e Smart Compound Sets on page 102 9 4 Compound Set Tools 104 Chapter 10 Tutorials Whether you are a brand new user of Chenomx NMR Suite or you have just upgraded from an earlier version the t
15. e Only apply line broadening after you are satisfied with the phasing and baseline correction in your spectrum e f you intend to apply reference deconvolution to your spectrum you can add line broadening at the same time See Reference Deconvolution on page 39 for details Related Topics Importing Spectra on page 13 Processing History Sidebar on page 34 e Phasing on page 36 5 4 Processing Tools 38 evomx Processing gt Advanced gt Reference Deconvolution Icon s AD Ctrl Alt 4 Menu Location Pe Cmd Alt 4 md Alt CHENOMX NMR SUITE USER MANUAL e Baseline Correction on page 37 e Reference Deconvolution on page 39 e Convert Spectra on page 41 Reference Deconvolution Reference deconvolution is a method of reconstructing an ideal spectrum by removing lineshape distortions based onthe shape of areference peak To successfully apply reference deconvolution to a spectrum you need to find a single isolated peak well separated from the signals in the rest of the spectrum If you have added DSS or TSP to your sample the methyl signal from either of these is an ideal choice Reference deconvolution is a linear process using direct and inverse Fourier transforms so quantitative relationships among compounds in the spectrum remain intact Applying reference deconvolution to a spectrum assumes that all lineshapes in the spectrum are affected by systematic distortions in the sa
16. e You can specify a minimum bin width of 0 00001 ppm and a maximum bin width equal to the width of the range that you have chosen For example if you are binning across a range of 2 to 10 ppm your maximum bin width is 8 ppm Related Topics Profiling Tools on page 46 6 5 Importing and Exporting Data 63 evomx CHENOMX NMR SUITE USER MANUAL Compound Set Tools on page 59 Send to Processor As you work with a spectrum in Profiler you may notice that the phasing baseline correction or other aspects of the spectrum s lineshapes are not properly adjusted Similarly you may import a spectrum directly into Profiler only to realize that it requires phasing baseline or other correction Send to Processor closes the current spectrum in Profiler and opens it in Processor retaining any changes you have made in Profiler Tips and Tricks e Any changes that you have made to the spectrum in Profiler are retained when you send the spectrum to Processor and are visible when you bring the spectrum back into Profiler However you still need to save the spectrum either in Processor or Profiler to permanently save those changes to the spectrum file Related Topics Chapter 5 Processor on page 28 6 6 Information Tools While profiling spectra you can view acquisition and sample information connected to the current spectrum and change the concentration units that appear in the Compound Table and any exporte
17. 0 4 Hz to the target linewidth during reference deconvolution instead of applying it in a separate step Click the Accept button to apply your changes to the spectrum Switch to the CSI Editor Once again since we have modified the processing of the spectrum it is a good practice to verify the fit of the CSI peak Click the Find Automatically button Determining the Spectrum pH Automatically 30 Switch to the pH Editor Setting the spectrum pH is very important Most of the Chenomx Reference Compounds are pH sensitive meaning their starting positions and transform windows are affected by the spectrum pH 10 2 Processor 108 evomx CHENOMX NMR SUITE USER MANUAL If you set a spectrum pH that differs a lot from the actual sample pH clusters will start farther then necessary from their real positions and the transform windows may notallow you to move each cluster far enough to compensate without overriding them 31 Click the Find Automatically button to have Processor attempt to determine the spectrum pH automatically Now that you have corrected the phasing and baseline of the spectrum automatic pH determination will work The calculated pH is 8 37 Determining the Spectrum pH Manually 32 Click and drag the pH slider bar to adjust the pH or manually enter a pH value in the pH text entry box The blue green and yellow lines indicating the positions of the imidazole creatinine and DFTMP peaks respect
18. Profiling a Spectrum on page 8 and Profiling Overlapped Regions in a Spectrum on page 11 Getting Started 1 OpenProfiler 2 Open the file called Samples Profiler Advanced Start cnx Although completely non overlapping compounds are easy to profile they cannot give any further insight into the shape of other compounds in the spectrum Profile these compounds first so that you can focus on the more challenging regions of the spectrum Since we covered the relevant techniques in Basic Profiling Techniques on page 110 they will not be covered in detail here Profiling Compounds using Basic Profiling Techniques 3 Using the basic techniques discussed in Basic Profiling Techniques on page 110 profile the following twelve compounds e 3 Indoxylsulfate 10 3 Profiler 112 evomx CHENOMX NMR SUITE USER MANUAL e 4 Hydroxy 3 methoxymandelate e Acetate e Citrate e Dimethylamine e DSS Chemical Shape Indicator Formate e Fumarate e Niacinamide e Pyruvate e Threonine e Trimethylamine Once you have profiled the non overlapped compounds a more systematic approach will help in profiling the remainder For this tutorial start at the right most edge of the spectrum and move to the left Fitting Compounds with Overlap 4 Zoom in on the two single peaks near 0 90 ppm These peaks correspond to methyl groups in the structure of pantothenate the highest Maximum Concentration in this region of the spec
19. USER MANUAL that you have applied to the current spectrum using Processor You can review this list to find out the parameters used in each layer like phase angles or reference deconvolution parameters and step back through past layers to reverse their effects When you import a processed spectrum Processor imports phasing baseline correction and other processing that you may have applied in other processing software The imported processing effects appear in the Processing History as a layer called Preprocessing The Preprocessing details appearing at the bottom of the panel indicate the format from which you imported the spectrum The Preprocessing layer is not reversible you cannot remove it How do I review and remove processing layers 1 Switch to the Processing History view in the Sidebar 2 Clickthe name ofa processing layer to review its associated parameters they appear in the Details box below the list 3 Click the Clear Last button to remove the most recent processing layer Click the button again to remove the next most recent layer and so on Or Click the Clear All button to remove all of the processing layers listed in the Processing History Tips and Tricks e The Processing History only tracks processing effects including phasing baseline correction reference deconvolution water deletion and line broadening Changes to spectrum metadata such as the spectrum details or CSI and pH settings do notappear
20. letting you review the complete contents of your library How do display the contents of a compound set 1 Selectthe set in the Compound Sets view The contents ofthe set appear in the Compound Table Tips and Tricks e You can drag compounds onto a Compound Set in the Compound Sets view to add them to the set You cannot drag compounds onto Smart Compound Sets e You can rename compound sets directly in the Compound Sets view Click on the name of a selected set type the new name and press Enter to accept the new name e Several operations involving compound sets are available by right clicking on them in the Compound Sets view Related Topics e Library Tools on page 96 Export Compounds on page 98 e Compound Sets on page 101 e Smart Compound Sets on page 102 e Rename Compound Sets on page 103 9 4 Compound Set Tools 100 evomx CHENOMX NMR SUITE USER MANUAL e Remove Compound Sets on page 103 Compound Sets Menu Location Icon s Hotkey s File New Compound Set D Ctrl N Cmd N Menu Location Compounds gt Add Selected Compounds to Compound Set Menu Location Hotkey s Compounds gt Remove Selected Compounds from gt Compound Set Delete You may need to create a compound set that does not change as you add new compounds to your library For example analysis of an extended dataset may require profiling a fixed set of comp
21. portable network graphic png 23 preprocessing 34 35 ACD Labs 5 CHENOMX NMR SUITE USER MANUAL Delta 5 Varian processed data phasefile 6 VNMR 5 VNMRj 5 XWIN NMR 5 preserve CSI area 31 previous spin definition 72 processed data Bruker 1r 13 JCAMP DX jdx 13 JEOL Delta jdf 13 NMRPipe ft2 13 Varian phasefile 13 processing baseline correction 37 history 34 history sidebar 18 34 line broadening 38 overview 8 phasing 36 preprocessing 34 35 reference deconvolution 39 reverse spectrum 41 supported spectra 5 see also supported file types water deletion 40 profiled compounds 46 48 49 50 52 53 57 61 profiled data 48 49 50 52 53 60 profiling best guess fit 121 compound line fit 117 determining concentrations 11 identifying compounds 9 no fit 121 overlapped regions 11 overview 8 subtraction line fit 118 sum line fit 119 water suppression 120 proline 125 131 134 proxy server 25 Q quick reference guide Compound Builder 78 Library Manager 95 Processor 29 Profiler 44 Spin Simulator 68 quick search 50 96 R redo zoom 20 Reference Compound Sets 3 59 reference deconvolution and line broadening 39 DSS TSP satellites 39 target linewidth 39 reference panel Compound Builder 91 Profiler 65 sidebar 18 65 91 relaxation delay 5 remove compound 99 compound from compound set 101 compound set 103 spectrum overlays 19 rename c
22. previously coupled spin definitions each split having the same J value as the original coupled J value e Most operations involving J modifiers are available by right clicking on a J modifier in the Simulation view Related Topics e Spin Systems on page 70 e Spin Definitions on page 71 e Simulation Sidebar on page 75 7 4 Information Tools While creating spin simulations you can view and update spin systems spin definitions and J modifiers associated with the current compound and view overall details on the current simulation Simulation Sidebar The Simulation Sidebar view contains Spin Definition Tabs which let you view and edit the properties of spin definitions and create edit or remove J modifiers How do edit spin definitions and J modifiers using the Simulation view Menu Location Icon s Hotkey s View Sidebar Simulation Ctrl Shift D Cmd Shift D 1 Selecta spin definition by clicking it in the Spectrum View or by selecting its tab in the Simulation view 2 Clickin any of the text fields and enter a new value to edit the number of protons center or width of the spin definition 3 Edit J modifiers by doing any of the following e Click Add to add a new J modifier to the current spin definition e Click Edit to edit the selected J modifier in the current spin definition Click Delete to delete the selected J modifier in the current spin definition Tips and Tricks
23. type 02 89 to find compounds appearing at 2 89 ppm or type 3 0 to 7 0 to find compounds appearing between 3 0 and 7 0 ppm You can reset the Quick Search box and clear all filters at any time by pressing Esc While editing the QuickSearch box press the down arrow to navigate to the Compound Table 6 3 Profiling Tools 51 evomx CHENOMX NMR SUITE USER MANUAL Related Topics e Spectrum View Tools on page 20 e Compound Table on page 46 e Compound Set Tools on page 59 Concentrations While profiling a spectrum you measure compound concentrations by determining heights of compounds signatures that best match peak heights in the current spectrum You can only adjust the concentration of the compound currently selected in the Compound Table Profiler determines the concentration of a compound using the standardized intensities si and standardized widths sw of its component peaks When you adjust the height of a compound the heights of all peaks and clusters corresponding to the compound scale proportionately When you have set a compound concentration to something other than unknown Profiler adds itto the Profiled Compounds set at the top ofthe Compound Sets view If you set a profiled compound s concentration to unknown Profiler removes the compound from the Profiled Compounds set How do I set compound concentrations 1 Selecta compound in the Compound Table If you do not see any compounds in the Co
24. 0394E 4 or 1 0384E 2 You may add a or character before any number indicating whether the following number is positive or negative if you use neither the number is assumed to be positive Numeric results of calculations are stored and displayed in double precision 64 bit You can use supported text variables in an expression Supported variables currently include ph returns the pH associated with the current spectrum as set in Processor true boolean equivalent to 1 and false boolean equivalent to 0 You cannot declare your own variables There are two types of mathematical operations available in expressions infix operations and prefix operations Infix operations involve an operator that occurs inside the two operands like 5 3 where 5 and 3 are the operands and is the operator Prefix operations involve an operator that occurs before the operands like cos 3 12 or max 1 100 where cos and max are operators and the contents of the parentheses are the operands 10 9 Using Expressions 135 ENOMX CHENOMX NMR SUITE USER MANUAL Table 10 3 Infix Operations Operation Description Examples Result Boolean Operations orgt Greater than ph 7 00 False for spectrum pH of 6 00 ph gt 7 00 true for 8 00 also false for 7 00 orlt Less than ph 7 00 True for spectrum pH of 6 00 ph 1t 7 00 false for 8 00 also false for 7 0
25. 2 Selectthe compounds that you would like to remove in the Compound Table 3 Click Remove Selected Compounds from Compound Set Tips and Tricks e When you change the contents of any compound set its name and icon in the Sidebar throbs for a couple seconds to indicate which set has changed If you have made a change that affects multiple compound sets all of the affected sets will throb e When you add new compounds you can choose to create Compound Sets containing the newly added compounds If the Compound Sets that would normally be created already exist the new compounds are added to the existing sets 9 4 Compound Set Tools 101 Enom File gt New Smart Compound Set Icon s D Menu Location Ctrl Shift N Cmd Shift N Hotkey s File gt Edit Smart Compound Set Icon s D Ctrl E Menu Location Hotkey s m md CHENOMX NMR SUITE USER MANUAL e Right click on a selected compound or group of compounds in the Compound Table and click Add to New Compound Set to create a new set containing the selected compounds e You can only remove compounds from Compound Sets and not Smart Compound Sets Related Topics e Library Tools on page 96 Export Compounds on page 98 e Compound Sets Sidebar on page 100 e Smart Compound Sets on page 102 e Rename Compound Sets on page 103 e Remove Compound Sets on page 103 Smart Compound Sets In Library Manager you can c
26. 5 Hz Notice that changing the height of either spin definition changes the height of the whole simulation you cannot obtain a perfect height match with all four spin definitions at the same time The discrepancy is normal and can be corrected in Compound Builder prior to adding the compound to your library see Simple Compound Valine on page 129 for details For now simply choose one ofthe spin definitions with which to fit the simulation height 10 5 Spin Simulator 124 CHENOMX NMR SUITE USER MANUAL 25 Save the simulation file If you would like to review the sample simulation of valine do not replace the file called Samples Spin Simulator Valine xss Complex Simulation Proline Now that you have developed a basic familiarity with some of the tools available in Spin Simulator you are ready to use them to simulate a more complex compound proline O di 6 4 So Son 5 N 1 H The spectrum of proline is much more complex than the spectrum of valine The protons at each position couple to all of the protons at adjacent positions Also the protons at each position are diastereotopic meaning that they can couple with each other geminal coupling as well as each coupling to adjacent protons While this means that splitting patterns will be based exclusively on doublets n 1 it also means that you need to be aware of a lot more coupling interactions Simulating Proline 1 Assign the spectrum matc
27. 7 1linux x86 sh to your desired installation folder 2 Run ChenomxNmrSuite 7 linux x86 sh 3 The install script creates a new folder named ChenomxNmrSuite you can run Chenomx NMR Suite by running the ChenomxNmrSuite sh script located in this folder 4 You have now installed Chenomx NMR Suite 1 1 Installation 1 evomx CHENOMX NMR SUITE USER MANUAL Linux 64 bit 4 Copy the installer script named ChenomxNmrSuite 7 0 linux x86 64 sh to your desired installation folder Run ChenomxNmrSuite 7 0 linux x86 64 sh A new folder named ChenomxNmrSuite is created you can run Chenomx NMR Suite by running the ChenomxNmrSuite sh script located in this folder You have now installed Chenomx NMR Suite 1 2 Activation and Licensing Chenomx NMR Suite uses an activation system designed to verify that Chenomx software products are legitimately licensed After you install the Chenomx NMR Suite software you need to activate it to ensure that you can use all ofthe modules that you purchased and that you can open edit and save changes to Chenomx file types cnx xcpd cnx1ib XSS To activate Chenomx NMR Suite Menu Location Icon s Help gt Software Activation A gj 1 Open any module of Chenomx NMR Suite If you have not previously activated or if your license has expired the Chenomx Software Activation dialog appears Otherwise on the Help menu click Software Activation
28. Author Author of the compound signature as you would like it to appear in the Compound Table in Profiler Magnet Frequency MHz Frequency of the acquired NMR spectrum in megahertz MHz Sample Concentration Concentration of the compound in the sample spectrum in mM millimoles per litre mM Last Modified Date and time at which the signature file was last modified and saved 8 4 Information Tools 91 CHE OMX NMR SUITE USER MANUAL UUID Universally Unique Identifier used to uniquely identify a particular signature in your compound library Reference Chenomx Compound ID InChI Code Chenomx compound ID associated with the compound IUPAC International Chemical Identifier InChI associated with the compound http www iupac org inchi Pulse Sequence SMILES Code Simplified Molecular Input Line Entry Specification SMILES associated with the compound Advanced Molecular Weight u Molecular weight of the compound in atomic mass units not including counter ions Pulse sequence used to acquire the sample spectrum that you would like to use as an reference overlay for the compound signature Valid pH pH value or range at which you expect the compound signature to be valid Comment Comment Text comments associated with the compound signature you can use this to record any additional information that you consider relevant Tips and Tricks e For accurate quant
29. Compound Builder Introduction You can use the Compound Builder module to build compound signatures that you can add to your library Although you can build compound signatures from scratch directly in Compound Builder you can build complex compounds more accurately if you simulate them in Spin Simulator first The simulation gives you a good starting point from which to build a high quality compound signature 10 6 Compound Builder 128 CHENOMX NMR SUITE USER MANUAL You can only complete the Compound Builder tutorial if you have purchased the Professional edition of Chenomx NMR Suite or if you are using the Evaluation edition of Chenomx NMR Suite Simple Compound Valine To become familiar with the various tools available in Compound Builder you will build a compound signature for a simple compound valine You can use the simulation that you created during the Spin Simulator tutorial or just use the Spin Simulator sample files provided If you have not yet completed the Spin Simulator tutorial you may find it helpful to do so before proceeding with Compound Builder 1 CH O c So NH The simulation of valine is a model representation of the expected spectrum for valine Compound Builder helps you to turn this model spectrum into a more accurate representation of an experimental spectrum For this purpose the four main areas you need to consider are refining the model simplifying the model and defining transform wi
30. Compound Table Click the pin next to the selection line in the Legend 4 How do I clear a pinned compound Menu Location Icon s Compound Selected Compound Clear Pin 1 2 Select the compound in the Compound Table In the Compound menu click Selected Compound Clear Pin clear the check box for the compound in the Pinned column click the red pin next to the selection line in the Legend or click the red X beside the compound s entry in the Legend Tips and Tricks Pinning a compound adds it to the Profiled Compounds set even if you have not set concentrations or transforms for the compound Pin settings are stored with the spectrum when you save itasa cnx file The compound that you pin remains pinned when you next open the file until you clear the pins You can export the pinned status of all compounds to a file using Export Profiled Data Related Topics Legend on page 17 Compound Table on page 46 Custom Colors on page 48 Starred Compounds on page 50 Legend Sidebar on page 64 6 3 Profiling Tools 49 evomx Menu Location Compound gt Selected Compound gt Clear gt Star Icon s amp Icon s X Ctrl L Hotkey s Cmd L CHENOMX NMR SUITE USER MANUAL Starred Compounds Starring compounds lets you mark them for future reference or to perform group operations on them including setting them to maximum concentrat
31. Double click again to close the Reference Panel Related Topics e Reference Panel on page 18 Preferences on page 25 e Profiling Tools on page 46 Spectrum Details Spectrum Details lets you view acquisition parameters for the current spectrum including VE File gt Spectrum Details sweep width magnet frequency pulse sequence and so on as well as user defined properties r3 such as sample pH and comments that have been added in Processor Icon s a 6 6 Information Tools 65 e CHENOMX NMR SUITE USER MANUAL Tips and Tricks e The information in Spectrum Details is read only in Profiler To change sample pH or add or modify comments for the spectrum send the spectrum to Processor Related Topics e Chapter 5 Processor on page 28 Concentration Units You can change the units of concentration used in the Compound Table Available units WEEEESSESSEE View gt Concentration Units include millimoles per litre mM micromoles per litre uM and milligrams per decilitre mg dL Tips and Tricks The maximum allowed concentration for any compound is 5000 mM 5 M When you select mg dL as the concentration unit the maximum value varies per compound since the units incorporate the molecular weight of the compound However the maximum value is always equivalent to 5000 mM e Concentrations in mg dL are only available for compounds whose molecular weight has been specified and the accuracy
32. Reference Deconvolution BP Une Broadening F r 8 5 Water Deletion O6 T 4 Shape Indicator CSI DSS Width Hz 1 017 Detail e Concentration mM 0 484 Height s 0 968 Center ppm 0 00000 Preserve CSI Area Find Automatically Switch to pHEditor_ i 1 l 799 81 MHz pH 8 37 2 47 ppm 2 o Sidebar View Buttons Let you change the currently visible Sidebar view Processing History Displays a list of every processing layer that you have applied to the current spectrum and lets you remove any processing layer that you have applied using the Processor module Information Panel Displays information relating to the current stage of spectrum processing Also contains the controls used during pH determination CSI adjustments and other processing steps Spectrum View Tools Let you navigate the spectrum more easily Spectrum View Displays the spectrum as well as guidelines used during pH determination CSI adjustments and other processing steps Spectrum Thumbnail Displays a thumbnail image of the current spectrum You can also use the thumbnail to navigate the spectrum at various zoom settings Status Bar Displays the current cursor position in the units specified by the View X Scale and View gt Y Scale settings Also displays information about recent user actions 6 5 1 Overview 28 CHENOMX NMR SUITE USER MANUAL 5 2 Quick Reference Guide Linux Windows Mac OS X
33. Select the compounds or compound set that you would like to export Open the Export Compound Pack dialog Enter a name for the exported compound pack The entered name is used to label the associated compound set when the compound pack is added to another library via Library Manager Click OK In the resulting file chooser locate the folder in which you would like to save the compound pack In the File Name field type the new name for the compound pack file The specified name can be different from the name of the compound pack itself but you may prefer to keep them the same Click Save How do export compounds to individual compound files Menu Location Icon s Compounds Export Selected Compoundsto Compound Files xcpd 1 2 Select the compounds or compound set that you would like to export On the Compounds menu click Export Selected Compounds to gt Compound Files xcpd In the resulting file chooser select the folder in which you would like to save the compound files Click Select 9 3 Library Tools 98 e CHENOMX NMR SUITE USER MANUAL Tips and Tricks e You and your collaborator each need a valid licensed copy or evaluation edition of Chenomx NMR Suite version 5 0 or later installed to make use of compound packs and signature files e Ifyou only want to export compounds that were actually profiled in a particular spectrum load the spectrum in Profiler and use Ex
34. Shift A E Software Activation 9 About Chenomx NMR Suite 7 3 Simulating Tools Spin Simulator provides you with a variety of tools to help you create accurate spin simulations by adding manipulating and removing spin definitions and coupling constants grouping spin definitions into spin systems selecting simulation algorithms and viewing summary details about your current simulation Spin simulation is a computationally intensive process and takes more time as the simulation you are creating becomes more complex Generally the amount of time required to recalculate a simulation increases more or less linearly with the number of spin definitions protons in the simulation and exponentially with the number of distinct J couplings Spin Simulator monitors the overall complexity of your simulation as you work and if you attempt to take an action that would result in unusable simulation times the action is cancelled and you see a warning dialog indicating that the resulting simulation would be too complex New Simulation New Simulation creates a new simulation file xss The new simulation file has the default simulation frequency of 800 MHz Tips and Tricks e The new simulation file does not have a spectrum overlay Add a spectrum overlay before you continue creating a simulation e You can overlay only one spectrum at a time in Spin Simulator e You need to save the new file to retain changes th
35. Spectrum View The results are the same as using the Show Entire Spectrum zoom tool Double click anywhere in the Spectrum Thumbnail to show the entire spectrum in the Spectrum View The results are the same as using the Show Entire Spectrum tool Related Topics e Show Entire Spectrum on page 20 Select Region You can use the Select Region tool as an alternate zoom function to specify areas with which to filter the Compound Table and to obtain information about the selected region itself including the region s width and the area under various lines within the region How do I select a region Maanosien co RAION 1 Activate Select Region View gt Zoom gt Select Region o ll lE 2 Click and drag across a region of the Spectrum View to select the region Icon s FRE 3 Double click in the selected region to expand the region horizontally to fill the Hotkey s Spectrum View md Or Middle click in the selected region to expand the region horizontally to fill the Spectrum View and apply an Auto Zoom How do I quickly select a region 1 Pressand hold down the Shift key 4 10 Spectrum View Tools 22 evomx CHENOMX NMR SUITE USER MANUAL 2 Click in the Spectrum View where you would like to start the selection then drag to the end point Tips and Tricks You can also activate Select Region by double clicking anywhere in the Spectrum View You must have a spectrum simulation or compoun
36. Topics e Spin Definitions on page 71 e Spin Navigator on page 73 e Simulation Sidebar on page 75 e Simulation Details on page 76 Spin Definitions Spin Simulator creates computer models of the interactions among the members of a spin system Within Spin Simulator you may consider a member of a spin system as equivalent to a single proton or a group of protons that are both chemical shift equivalent and magnetic equivalent Spin definitons described the members of spin systems and are the basic building blocks of the models created by Spin Simulator A spin definition consists of three basic pieces of information The number of protons represented by the spin definition the center of the spin definition in ppm equivalent to a chemical shift in an NMR spectrum and a width in sw analogous to a linewidth at half height in an NMR spectrum You can organize spin definitions into spin systems as described elsewhere in this chapter see Spin Systems on page 70 How do add a new spin definition Menu Location iip gt Add New spin 1 Open the Add New Spin Definition dialog efinition ean Oj 2 Enter a number of protons starting center in ppm and starting width in sw You can change the entered values later Ctrl D FORES enin 3 Click OK 7 3 Simulating Tools 71 Enom CHENOMX NMR SUITE USER MANUAL How do I edit a spin definition 1 Select the spin definition by clicking on itin
37. a smaller region adding more peaks manually or simulating the compound in Spin Simulator and importing the simulation Related Topics e Select Region on page 22 e Add Peak on page 81 e Selecting Peaks and Clusters on page 82 e Adjusting Peaks on page 83 e Optimize Selected Peak Shapes on page 85 Transform Windows You can limit the amount that you can transform or move individual clusters ina compound signature in Profiler using transform windows Establishing transform windows for your own compounds improves the quality of profiles that you perform with your custom compound signatures If you set transform windows manually ensure that they are wide enough to account for the degree of variability in cluster position that you expect to see in your samples For example if you routinely analyze spectra with widely varying pH you will need larger transform windows than if your sample spectra are always close to the same pH The most common influences on the position of a cluster in a compound are pH and ion concentrations To manually set accurate transform windows for a compound consider acquiring spectra of the pure compound at the outer limits of the conditions you expect to 8 3 Building Tools 86 evxomx CHENOMX NMR SUITE USER MANUAL encounter when profiling the compounds in experimental mixtures The additional spectra let you map the maximum extent of these effects on the cluster positions in your com
38. and clusters in the lists in the Information Panel Hold down the Ctrl or Cmd keys while clicking on the desired peaks and clusters e Ifyou do not have a spectrum overlay the Information Panel indicates that your compound signature is in the default environment When you overlay a spectrum the environment changes to match the overlay The Information Panel displays a warning if your spectrum overlay does not match the information that you provided in the Compound Details You need to update the Compound Details to match the overlay or choose a new overlay spectrum to remove the warning Related Topics e Spectrum Overlays on page 19 e Building Tools on page 80 e Compound Details on page 91 8 4 Information Tools 93 Chapter 9 Library Manager The Library Manager modulelets you create and modify compound sets based on compounds in your library as well as compounds that you have created in Compound Builder You can use compound sets in Profiler to focus your profiling efforts on specific compounds based on dynamic filters or predefined lists of compounds 9 1 Overview File Edit View Library ib All Compounds h Quecseanh Cer 6 B chrenom 0 mz Compound Name Frequency MHz Valid pH Version Compound Comment Putrescine 800 00 4 06 to 8 99 13 May 2009 2007 Chenomx Inc B chrenom 500 miz Pyridoxine 800 00 3 98 to 9 05 03 Apr 2009 2005 Chenomx Inc 9
39. certain range of frequencies see Quick Searches on page 50 To quickly filter based on a single location right click on the spectrum and click Filter for Compounds Near x xx ppm to select a single frequency Similarly to filter based on a frequency range select a region then right click inside the selected region and click Filter for Compounds in Selected Region The frequency filters display all compounds that have transform windows overlapping the selected frequency or frequency range Since transform windows are a function of spectrum pH the number of compounds displayed using the frequency filters varies based on your spectrum pH Text Filters You can filter the Compound Table based on a simple text search by typing the text to search for in the empty text box at the top right corner of the Compound Table Filtering can help you look for a particular compound or a group of compounds with similar names like all compounds containing acetate 10 4 Targeted Profiling 116 evomx CHENOMX NMR SUITE USER MANUAL You can also use text filters to type in frequency searches see Frequency Filters on page 116 To search for compounds near 1 90 ppm type 1 90 in the text box without the quotes To search for compounds from 2 75 to 4 30 ppm type 2 75 to 4 30 without the quotes Compound Lists Alist of compounds known to occur in samples of the type that you are analyzing can be an invaluable tool to guide you
40. click the Cancel button to discard them Tips and Tricks Only phase your spectrum once If you do not like the results of phasing undo it or remove it using the Processing History then try again Always phase your spectrum before applying baseline correction or any other processing layers Select one of the phase angle controls and use the arrow keys to make fine adjustments to the phase angle The arrow keys adjust in increments of 1 in normal mode 0 1 in fine mode and 0 01 in very fine mode Properly phase all of your spectra as good phasing is essential to accurately analyzing your data using Chenomx NMR Suite Your spectrum is properly phased when it has a baseline that describes a smooth curve across the entire width of the spectrum In spectra of aqueous samples the water peak may be distorted relative to the rest of the spectrum do not use the water peak to determine phasing Instead try to obtain smooth baseline curves to either side of the water peak You will usually need to adjust the zero order phase angle more than the first order phase angle but remember that the requirements of a specific spectrum may vary 5 4 Processing Tools 36 CHENOMX NMR SUITE USER MANUAL e During a phasing session you can clear your current adjustments by clicking the Reset button After you have accepted your changes you can clear previous adjustments through the Processing History panel Related Topics Importin
41. color model RGB Hex sa scalable vector graphics select region Processing layer available in Processor Lets you reconstruct an ideal spectrum by removing lineshape distortions caused by systematic variations in the magnetic field of the spectrometer Sidebar view that displays additional data for the compound currently selected in the Compound Table in Profiler or for the compound ID specified in the compound details in Compound Builder if any Refers to a pause preceding active data collection in an NMR pulse sequence to ensure that residual signal from the radiofrequency pulse used to excite the sample is not visible in the spectrum The recommended relaxation delay for spectra intended for use with Chenomx NMR Suite is 1 s Variation of spectral binning in which the subtraction line is binned instead of the spectrum line Processing layer available in Processor Inverts the order of the data points in a spectrum in the frequency domain effectively flipping the spectrum horizontally Only necessary for spectra from certain Bruker spectrometers Additive color model used to represent color as a combination of red green and blue light for display on electronic devices compare the subtractive CMYK color model used to reproduce color in print Usually encoded for computer programs as a triplet of 8 bit unsigned integers one for each color represented in decimal 0 to 255 or hexadecimal 00 to FF notation where 0 or
42. concentrations when available in Profiler In Spin Simulator a J modifier that links two spin definitions via a common split count and J value resulting in more accurate calculation of complex coupling interactions Equivalent to J couplings in previous versions of Chenomx NMR Suite pH indicator supported by Chenomx NMR Suite Most accurate for pH 3 75 to 5 50 See chemical shift and shape indicator Mode in Processor that lets you define the properties of the CSI foraspectrum including the experimental concentration in mM peak center in ppm height in si and width in Hz In Processor the line in the Spectrum View illustrating the current CSI settings as defined in the CSI editor In Compound Builder the limits applied to a cluster when such limits are not otherwise specified e g through the menu item Compound Transform Window Set Default on Selected Clusters Equivalent to a range of 0 006 ppm centered on the 143 evomx CHENOMX NMR SUITE USER MANUAL Delta DFTMP DSS eps encapsulated PostScript file exporting spectrum graphic exporting profiled compounds exporting profiled data fid fid fit automatically fit percentages frequency domain size frequency filter position of the cluster when the default is applied or 0 003 ppm in either direction NMR software package developed by JEOL to run their spectrometers and process the resulting data Abbreviation of
43. difluoro trimethylsilyl methyl phosphonate a pH indicator supported by Chenomx NMR Suite Most accurate for pH 5 00 to 7 50 Abbreviation of 2 2 dimethyl 2 silapentane 5 sulfonate the CSI recommended by Chenomx for most samples All other CSIs in Chenomx NMR Suite are defined relative to DSS See encapsulated PostScript file PostScript file which contains image size and layoutinformation according to Adobe s Document Structuring Convention Used primarily for electronic and professional desktop publishing In Profiler refers to creating an image file showing the current Spectrum View Used to generate images in various formats for use in presentations or publications In Profiler refers to creating a compound pack file pack or set of compound files xcpd based on profiled compounds in the currently open spectrum In Profiler refers to creating a tab delimited text file describing the data stored in one or more profiled Chenomx spectrum files cnx The resulting file is suitable for use in a variety of statistical analysis and spreadsheet software See NMRPipe spectrum data See spectrum data In Profiler function that provides suggested concentration and transforms for the currently selected compound In Profiler the percentage of the area under the spectrum line in the selected region Reported for the spectrum line and the sum line The number of data points in a Chenomx spectrum after importing spectru
44. either in the Spectrum View the Information Panel or both Tips and Tricks e When you have a cluster currently selected only the peaks associated with that cluster are available to select via the Information Panel e When you have no clusters currently selected no peaks are visible or available to select via the Information Panel e Ifthe peak that you would like to select is not visible in the Information Panel you may need to select a different cluster Related Topics e Add Peak on page 81 8 3 Building Tools 82 CHENOMX NMR SUITE USER MANUAL e Delete Selected Peaks on page 83 e Adjusting Peaks on page 83 e Grouping Peaks as a Cluster on page 84 e Optimize Selected Peak Shapes on page 85 e Generate Cluster for Region on page 86 e Transform Windows on page 86 e Cluster Navigator on page 90 e Information Panel on page 92 Delete Selected Peaks As you build a compound signature you may need to delete one or more peaks from the signature to refine or simplify the signature You can delete one or more selected peaks from the current signature including peaks in different clusters whole clusters or multiple clusters How do I delete peaks Menu Location Icon s Hotkey s ML Ho 1 Selectthe peaks or clusters that you would like to delete 4g 2 Click Delete Selected Peaks Delete Tips and Tricks Delete You can delete multiple peaks or c
45. fid while the processed data is stored in the file named Example fid datdir phasefile e Ifyou are opening a Bruker spectrum named ExampleM1 the raw data is stored in the file named Example 1 fid while the processed data is stored in the file named Example 1 pdata 1 t1r 4 2 Importing Spectra When you open a spectrum in a supported non Chenomx format in Processor or Profiler you need to select import options for conversion into the Chenomx spectrum format cnx You can import raw spectrum data in Varian fid Bruker fid JEOL jdf or NMRPipe fid file formats and processed spectra in Varian phasefile Bruker 1r JEOL jdf NMRPipe ft2 or JCAMP DX jdx file formats When you import processed spectra your import options are somewhat limited since most ofthe processing that you may want to apply is assumed to have already taken place 4 1 Opening Files 13 evomx CHENOMX NMR SUITE USER MANUAL Table 4 1 Import NMR Data Options CSI Concentration mM pH Automatic pH Advanced Details Defaults Specify the Chemical Shape Indicator CSI used in the sample You can choose DSS TSP or formate Enter the concentration of the specified CSI in millimoles per litre Attempt to automatically detect the pH of the sample subject to the specified uncertainty using signals from imidazole creatinine and DFTMP You must haveat least one of these pH indicators present in the sample to attem
46. have just undone If you undo a change then make other changes you can no longer redo the change that was undone 4 7 Change Columns In modules that have Compound Tables Profiler and Library Manager you can specify which of the available columns are visible in the Compound Table How do I change the visible columns in the Compound Table Menu Location View Change Columns 1 Open the Change Columns dialog pu US 2 Select the check boxes for the columns you would like to display and clear the check boxes for the columns you would like to hide 3 ClickOK Tips and Tricks You can quickly display or hide a particular column by right clicking in the header row of the Compound Table and clicking the column that you would like to display or hide e The Concentration Maximum Autofit Clusters Matched Clusters Color Pinned Starred and Transforms columns are only available in Profiler 4 8 Sidebar The Sidebar is a dedicated area of the screen used to display frequently used information Manu locctan View gt Show Sidebar related to the Spectrum View Several views are available in the Sidebar depending on the module currently in use Available views include Legend all modules except Library oe EL Elat Manager Reference Panel Profiler and Compound Builder Compound Sets Profiler TT Ctrl Shift S Simulation Spin Simulator and Processing History Processor otkey s Cmd Shift S Related Topics e Information Tools on page 30
47. need to add the spin definitions in the indicated order to complete the tutorial doing so will make the tutorial easier to understand since the Spin Definition SD notation appears throughout this tutorial for clarity 5 Zoom in to SD6 4 121 ppm 6 Measure the two coupling constants represented in this region of the spectrum using the spectrum line black as your reference Specifically find the distances from an outermost peak to the adjacent peak and from an outermost peak to the second peak in The distances in this spectrum are 8 79 Hz and 6 52 Hz 7 Add one J modifier to SD6 for each of the measured distances Use uncoupled splits with split counts of 1 and J values of 8 79 and 6 52 Hz You know that each of these couplings will link to single protons so you can use a split count of 1 for each of them 8 Adjust the frequency height and width of SD6 to better fit the spectrum 9 Ifyou need to adjust the J values for SD6 select the J modifier in the Simulation view and use the J Value Editor appearing under the Spin Navigator to fine tune the J value 10 Zoom in to SD4 and SD5 Based on the assignment above there are three coupling constants associated with each of these spin definitions One can be easily measured as the distance between an outermost peak and the second peak in this measurement yields around 11 58 Hz for both spin definitions suggesting that this is the coupling constant linking these two spin de
48. quality of the source signatures and in particular the master signature Creating a pH sensitive version of valine 1 Open Compound Builder 2 Open the valine signature If you have already completed the Compound Builder tutorial open the signature that you built Otherwise open the sample signature called Samples Compound Builder Valine xcpd 3 Overlay the valine spectrum called Samples Compound Builder Valine cnx 10 7 Building pH Sensitive Compounds 133 evomx CHENOMX NMR SUITE USER MANUAL 10 11 Open the pH Sensitivities dialog Click Load Data Points Select the folder called Samples Compound Builder pH Data Points and click Set Data Points Use the tabs at the top of the window to review each cluster The red dots representing the loaded data points should appear in a reasonably shaped curve Click Optimize Lines Review each cluster again Ensure that the blue line representing the cluster centers and the dotted gray lines representing the transform windows are reasonable and pass through or close to the red data points When you are satisfied with the proposed fit click Accept Save the compound file If you would like to review the sample pH sensitive signature for valine do not replace the file called Samples Compound Builder Valine pH xcpd 10 8 Library Manager Introduction You can use the Library Manager module to add new compounds to your library remove existing compounds a
49. samples Then when this urine compound set is the only one active any quick searches that you perform will only return compounds that appear in urine samples as potential hits Acompound set called Profiled Compounds always appears atthe top ofthe Compound Sets view in Profiler The Profiled Compounds set includes all compounds in the current spectrum that have been modified based on concentrations transforms custom colors pins and stars The Profiled Compounds set updates continuously so if you clear the concentration ofa compound it immediately disappears from Profiled Compounds In this case you can still select the compound from its original compound set If you change the contents of a compound set in Library Manager your changes immediately appear in Profiler including modified selection rules for Smart Compound Sets manual changes to Compound Sets by adding or removing compounds and created or deleted compound sets Related Topics Profiling Tools on page 46 Open Library Manager on page 59 Open Library Manager While profiling a spectrum you may want to define a new compound set that contains a Menu Location Icon s Hotkey s File Open Library Manager amp Ctrl B Cmd B smaller list of compounds or modify an existing compound set to focus more directly on your current project To access and edit compound sets you can open the Library Manager module from Profiler Tips and Tric
50. serene EE E ee hares 98 Send to Compound Builder sicccicccivescesdcencodestexcesndsagenisntanecuniieeccdestvecesnids 99 Remove Selected Compounds cccceeeeeeeeeeeeeeeeeeeaeeea essa eeae esa eeaeeaees 99 9 4 Compound Set Tools eiie ien ctantleneceactencaadcceccusd iaa a aiii 100 Compound Sets Sidebar srice eE 100 COMP OUNG Sets acinis etie ne ocncdivectdantencdenbcuecdiccaneqamaswesideateaades 101 Smart Compound Sets crnci enesis eea eoi EEEE 102 Rename Compound Sets sssssssessesseseeeenee eene iaaa aE 103 Remove Compound Sets e rie Eee ea E HERI I e E te ME ORER ERR EUX EAR ERES 103 LO Tutorials ieoi 105 10 1 File Location Note x tr tr kt nt aan na SX EE FERE XU ORA Lc ERR UNE 105 IK acitogm m RB die 105 Introduction ertt eei rx ete Ern ks o rex edes prse c kso nese dte ERE EEUEEER EE 105 Processing a SDectrUTI iusisecseese uxo eeesskcc esce xu sensa cerise oa wgasa ei RES sd E rE o AE 106 10 3 Profiler TUUM 110 livisgerstoa tr 110 CHENOMX NMR SUITE USER MANUAL Basic Profiling Techniques ss sssssssssserseresrsrrerrerrnrserrnrterrrrnrnrrerrnrrnns 110 Advanced Profiling Techniques sesseeeeem mm 112 10 4 Targeted Profiling ient code ee mx one ia x xoc es bi A EEA 116 Identifying Compounds eerie meon aE XR n EE 116 Profiling Clusters denuo eitnesuni nex reise cns kd PR RI chiatanaesite
51. small dataset of five or ten spectra first before moving on to larger datasets The time needed for the smaller dataset will help you to more accurately estimate the time needed to complete a binning session If you choose one or more folders as the source binning only includes spectra both directly in the specified folders and in subfolders ofthe specified folders If you do not explicitly specify a target folder output files are created in the folder containing your source spectra Binning based on number of bins divides the spectrum into the specified number of bins after excluding the regions that you have defined if any To do residual binning each ofthe source spectra must have been analyzed in Profiler and must contain at least one compound with a defined concentration Excluding regions from a binning dataset can help you to remove the influence of interfering or confounding signals Normalization based on total area gives the area of a particular bin as a fraction of the total area of all bins except area in any ofthe excluded regions that you may have defined Spectral binning is subject to several numerical limits e Each binning session can include a maximum of 5000 spectra e The range that you define when using number of bins or size of bins as a binning method must be at least 1 ppm wide and can be as large as 1998 ppm 999 to 999 ppm e You can specify a maximum of 1000000 one million bins or a minimum of 1
52. spectrum pH If your sample does not contain these compounds or if you prefer to use an externally measured pH you may enter a pH value manually While importing a spectrum Processor attempts to calculate the pH of the sample automatically using the frequencies ofthe imidazole creatinine and DFTMP peaks You can refine or change this calculated pH in the pH Editor If Processor cannot calculate the pH of your sample you need to set it manually Whether you use automatic or manual methods to set the spectrum pH you can also set an uncertainty for the pH value The pH uncertainty helps to determine the size ofthe transform windows for pH sensitive signatures in Profiler Simin 7 2 H pK l e p pKa logio rm Figure 5 1 Equation to calculate spectrum pH from the position of a single peak pKa is the acid dissociation constant of the indicator is the chemical shift of the peak and 6 and min are the upper and lower bounds on the chemical shift Processor calculates the spectrum pH as a function of the peak positions of the indicator compounds The formula used for DFTMP calculates spectrum pH based on the observed position of a single peak see Figure 5 1 on page 32 while the formula used for both imidazole and creatinine uses the distance between the two observed peaks see Figure 5 2 on page 32 H 2 pKa 4 ml lo z p p 810 AB AL Figure 5 2 Equation to calculate spectrum pH from the positions of two peaks pKa is
53. systematic influences on compound concentrations How do scale the concentrations of all compounds by a common factor Compound All Compounds Menu Location i Scale Concentrations Icon s Ha 1 On the Compound menu click All Compounds gt Scale Concentrations 2 Enter the multiplication factor you would like to use To increase concentrations use a factor greater than one To decrease them use a factor less than one 3 ClickOK How do I scale the concentrations of starred compounds by a common factor Compound Starred Menu Location Compounds Scale Concentrations I Icon s H 1 Star atleast one compound 2 On the Compound menu click Starred Compounds gt Scale Concentrations 3 Enter the multiplication factor you would like to use To increase concentrations use a factor greater than one To decrease them use a factor less than one 4 ClickOK 6 3 Profiling Tools 57 evomx CHENOMX NMR SUITE USER MANUAL Tips and Tricks If you enter a multiplication factor that would result in a concentration higher than 5000 mM for any compounds those compounds are set to 5000 mM All other compounds scale with the exact factor entered If you set the multiplication factor to zero all of the profiled compounds are set to 0 mM Scale Concentrations does not affect compounds with unknown concentrations Related Topics Starred Compounds on page 5
54. target linewidth larger than the native linewidth in your spectrum is equivalent to applying line broadening Choosing a value smaller than the native linewidth may provide some resolution enhancement at the expense of a reduced signal to noise ratio and possible spectral artifacts 5 4 Processing Tools 39 exomx Menu Location Icon s Hotkey s Processing Advanced Water Deletion Wo Ctrl Alt 5 Cmd Alt 5 CHENOMX NMR SUITE USER MANUAL Related Topics e Importing Spectra on page 13 Processing History Sidebar on page 34 e Phasing on page 36 e Baseline Correction on page 37 e Line Broadening on page 38 e Convert Spectra on page 41 Water Deletion In many spectra of biofluids or cell extracts the water peak may be very large In some cases it is so large that seeing any other peaks while completely zoomed out is difficult Water deletion is a simple processing layer that masks data points in the frequency domain across a range associated with water It is designed to prevent the height of the water peak from dominating the vertical range of the spectrum display Using water deletion is optional Ensure that no peaks of interest occur close to the water peak before you apply water deletion as such peaks may be masked by the water deletion layer Apply water deletion after any other processing layers including phasing baseline correction and reference deconvolution Whi
55. the Spectrum View or selecting its Spin Definition Tab in the Simulation view Do any of the following e Click and drag the blue triangle on the horizontal axis to change the center of the spin definition e Click and drag the blue triangle on the vertical axis to change the height of the simulation e Click and drag the spin definition directly in the Spectrum View to change its center and the simulation height simultaneously e Click and drag the blue triangles on either edge of the spin definition at around half the height of the tallest peak to change the width ofthe spin definition e Use the W and S keys or the up and down arrow keys to adjust the height of the whole simulation up and down e Use the A and D keys or the left and right arrow keys to adjust the position of the selected spin definitions left and right Usethe Q and E keys to display the next or previous spin definition How do I delete a spin definition Menu Location Icon s Simulation Delete Current Spin Definition ex 1 2 Select a spin definition using the Simulation view or the Spin Navigator Click Delete Current Spin Definition Tips and Tricks A spin definition can describe no more than ten protons However given that a spin definition typically describes chemically and magnetically equivalent protons you may find that a value greater than three a methyl group is not often necessary A spin system can co
56. the magnitude ofthe split defined by a J modifier Equivalent to a coupling constant for coupled splits In Spin Simulator a graphical control that lets you vary the J value for the currently selected J modifier Sidebar view providing an interactive display of the various lines appearing in the Spectrum View Pool of compound signatures xcpd available for use in Chenomx NMR Suite The Library replaces the Chenomx Compound Libraries available in previous versions of Chenomx NMR Suite Module in Chenomx NMR Suite that lets you manage your Library by addingor removing compounds updating existing compounds with new versions and creating updating and deleting compound sets Chenomx file format cnxlic used to activate Chenomx NMR Suite Processing layer available in Processor A mathematical operation that multiplies a fid by an exponential function in the time domain averaging out instrumental noise at the expense of increasing linewidths The exponential function is represented by a value measured in Hz approximately corresponding to the increase in linewidth that will result from the operation Describes a relationship within a molecule between nuclei that couple equally to any nucleus in the same spin system Nuclei that are magnetic equivalent are chemical shift equivalent by definition Calculated value visible in the Compound Table and exportable using Export Profiled Data the matched clusters for a compound are clust
57. to 1 3 Hz is sufficient Select SD1 1 031 ppm Add a J modifier to SD1 Use a J value of 7 07 Hz and select Uncoupled Split with a split count of 1 Adjust SD1 to fit the spectrum Once again a width of 1 2 to 1 3 Hz is sufficient Zoom to SD3 3 604 ppm using the Spin Navigator or the Spin Definition pane Measure the distance between peaks in the doublet This doublet measures about 4 36 Hz Add a J modifier to SD3 Use a J value of 4 36 Hz and select Uncoupled Split with a split count of 1 Adjust SD3 to fit the spectrum This doublet has a width of around 1 1 Hz Zoom to SD2 2 264 ppm using the Spin Navigator or the Spin Definition pane The resulting view does not reveal much of the actual spectrum so adjust it to get a better view Click View Zoom Set Zoom and enter 2 23 to 2 30 ppm for the X Axis and 0 05 to 0 87 si for the Y Axis Add a J modifier to SD2 Select Coupled to Spin Definition 0 using the uncoupled split of 7 02 Hz The spin definition is now linked to one ofthe methyl groups notice that it has split to a quartet n 3 Add two more J modifiers one coupled to SD1 using the uncoupled split of 7 07 Hz and the other coupled to Spin Definition 3 using the uncoupled split of 4 36 Hz Notice that with each added J modifier the spin definition becomes more complex and matches more closely with the spectrum Adjust SD2 to better fit the spectrum This spin definition has a width of about 1
58. to have Processor reverse the spectrum automatically After importing a spectrum you can reversethe spectrum manually In either case a Reverse Spectrum layer appears in the Processing History panel you can remove this layer if necessary Tips and Tricks e Ifyou notice that a spectrum from a particular spectrometer must be reversed it is likely that all spectra from that instrument especially those acquired with the same parameters need to be reversed e fitis necessary apply Reverse Spectrum first as other processing layers may be difficult to apply correctly when the spectrum is backwards Related Topics Importing Spectra on page 13 e CSI Editor on page 31 Processing History Sidebar on page 34 e Convert Spectra on page 41 5 5 Importing and Exporting Data Processor can help you to efficiently importraw spectral data from various sources convert them into Chenomx spectra cnx and begin working with them Convert Spectra For larger projects you may want to convert groups of spectra into Chenomx spectra cnx processing them with a consistent set of parameters to ensure consistent analysis results How do I convert a group of spectra Menu Location Tools Convert Spectra 1 Start the Convert Spectra wizard EA feu da 2 Choose the source spectra to convert The source spectra must be in one of the supported file formats Spectral Data Processing on page 5 3 Ifthe source spectra include multiple fil
59. transform applied to the cluster The information appears in the top right corner of the Spectrum View and visually as a thick blue line connecting the starting position of the cluster and its current position If the cluster is not transformed the display reads Cluster is not transformed and no visual indicator appears When you transform a cluster outside its transform window its transform adjustment triangle turns red Also when you hover over the cluster or its triangle the visual indicator for the transform is red as is the text in the top right corner ofthe Spectrum View describing the extent of the transform To clear all of the transforms for the current spectrum select Compound gt All Compounds Clear Transforms To clear transforms only for starred compounds select Compound Starred Compounds Clear Transforms You can see which compounds have been transformed by turning on the Transform column in the Compound Table The Transform column will also indicate whether the compound has any clusters that have been transformed beyond their transform windows You can export a file describing the transform status of all compounds using Export Profiled Data 6 3 Profiling Tools 54 CHENOMX NMR SUITE USER MANUAL Related Topics e Spectrum View Tools on page 20 e Compound Table on page 46 e Starred Compounds on page 50 e Quick Searches on page 50 e Concentrations on page 52 e
60. 0 Concentrations on page 52 Compound Set Tools on page 59 Cluster Navigator The Cluster Navigator lets you move quickly among the clusters of the currently displayed compound It appears in the top left corner of the Spectrum View as an ordered list of the approximate positions of all the clusters of the compound in ppm When you click ona cluster position the view zooms to provide an optimal view of the cluster including the larger of the full transform range of the cluster or the full width of the cluster and the full vertical extent of any peaks within the horizontal range You can also use the Cluster Navigator to move sequentially through the list of clusters in either direction How do I display the clusters of a compound in the Spectrum View Menu Location View gt Show Cluster Navigator 1 Ctrl Shift N Hotkey s Cmd Shift N 2 Make sure that the Cluster Navigator is visible and select a compound in the Compound Table Click a cluster position to zoom directly to that cluster Click the left or right arrow to move sequentially through the list of clusters Tips and Tricks Use the Q and E keys to display the next or previous cluster Clusters that appear green in the Cluster Navigator are matched meaning they closely match the spectrum line as determined by comparing the sum line red and the spectrum line black near each cluster You can click on a cluster and drag along the Cluster Navigator to
61. 0 gt orgte Greater than or equal to ph 7 00 False for spectrum pH of 6 00 ph gte 7 00 true for 8 00 also true for 7 00 orlte Lessthan or equal to ph lt 7 00 True for spectrum pH of 6 00 ph Ite 7 00 false for 8 00 also true for 7 00 or Equal to use with care when dealing ph 7 00 True for spectrum pH of 7 00 with non integer values ph 7 00 false for anything else l Not equal to ph 7 00 False for spectrum pH of 7 00 true for anything else Mathematical Operations Addition 3 202 5 47 8 672 1 204E 4 4 473E 4 5 677E 4 Subtraction 9 01 2 356 6 654 5 469E2 1 24E2 422 9 Multiplication 1 0438 3 389 3 5374382 5 469E2 1 248E2 68253 12 Division returning a value with a 5 3 1 6666666666666667 decimal component 7 20 3 20 225 Integer division rounds operands to 5 3 1 ud aaa z away the remainder Integer modulo rounds operands to 5 3 2 ee ae division Exponentiation the first operand is 5 3 125 raised to the power of the second operand Table 10 4 Prefix Operations Operation Description Examples Results Logical Operations and arg1 arg2 Returns true if and only if both and ph 7 00 ph True for spectrum pH of 6 00 supplied values are true returns lt 7 65 false for 8 00 false otherwise if arg1 arg2 arg3 Based on the criterion arg1 if ph lt 2 103 for spectrum pH of 6 00 returns arg2 if arg1 is true returns arg3 otherwise 7 00 2 103 3 032 3 032 for 8 00 not arg
62. 00 represents no contribution from a color while 255 or FF represents maximum contribution In Profiler colors are expressed as 6 digit hexadecimal numbers two digits each for red green and blue in that order Using this system red is expressed as FF0000 green as 00FF00 and blue as 0000FF More complex colors can also be expressed using this notation 6495ED is cornflower blue while FF69B4 is hot pink See RGB color model See standardized area Open standard created by the World Wide Web Consortium XML based format for describing two dimensional vector graphics Suitable for image distribution on the internet Tool that lets you temporarily mark a specific region of the spectrum in the Spectrum View Allows more precise zooming defining frequency ranges for quick searches measuring areas under various lines marking clusters peaks or spin definitions for selection marking a region in which to generate a new cluster and so on 150 evomx CHENOMX NMR SUITE USER MANUAL selection line send to Compound Builder send to Processor send to Profiler si Sidebar simplified molecular input line entry specification Simulation simulation details simulation file simulation line smart compound set SMILES spectral binning Line in the Spectrum View in Compound Builder and Spin Simulator corresponding to the currently selected peak cluster or spin definition colored blue by default
63. 1 Returns true if the supplied value is false and false if it is true not ph 8 00 True for spectrum pH of 6 00 false for 8 00 10 9 Using Expressions 136 ENOMX Operation or arg1 arg2 CHENOMX NMR SUITE USER MANUAL Description Returns false if and only if both supplied values are false returns true otherwise Examples or ph 1t 6 ph gt 8 Results True for spectrum pH of 4 00 or 9 00 false for 7 00 Mathematical Operations abs arg1 Returns the absolute value of abs 3 2084 3 2084 the supplied argument abs 1 391 1391 ceil arg1 Returns the smallest integer ceil 3 2084 4 SEU notless than the supplied ceil 1 391 4 exp arg1 Returns Euler s number e exp 1 2 7182818284590455 e raised to the power of the supplied value floor arg1 Returns the largest integer that floor 3 2084 3 is not greater than the supplied floor 1 391 2 value log arg1 Returns the base 10 logarithm log 10 1 ofthe supplied value logn arg1 Returns the base e natural logn 2 71828 0 999999327347282 1 logarithm of the supplied value max arg1 arg2 Returns the greater of the two max 2 23 4 30 4 30 SUBPUSU AES max 2 23 4 30 2 23 min arg1 arg2 Returns the smaller of the two min 2 23 4 30 2 23 supplied yates min 2 23 4 30 4 30 pow arg1 arg2 Returns the first supplied value pow 5 3 125 raised to the power of the second supplied value equivale
64. 1 evomx CHENOMX NMR SUITE USER MANUAL Related Topics e Selecting Peaks and Clusters on page 82 e Delete Selected Peaks on page 83 e Adjusting Peaks on page 83 e Grouping Peaks as a Cluster on page 84 e Optimize Selected Peak Shapes on page 85 e Generate Cluster for Region on page 86 Transform Windows on page 86 e Cluster Navigator on page 90 e Information Panel on page 92 Selecting Peaks and Clusters Many actions that you may perform in Compound Builder require you to select a peak or cluster to act on There are several ways to select peaks unassociated groups of peaks or clusters Clicking on the graph selects either peaks or clusters You can toggle between selecting peaks or clusters via the graph itself butthe Information Panel always lets you select either How do I select a cluster Menu Location Hotkey s Select by Cluster Ctrl B Cmd B 1 Turnon selection by cluster 2 Clickonthecluster in the Spectrum View Alternately click on the cluster s position in the Information Panel or double click on any peak in the cluster How do I select a peak 1 Turn off selection by cluster 2 Clickonthe peak in the Spectrum View Alternately click on the peak s position in the Information Panel How do I select multiple peaks or clusters 1 Turn selection by cluster on or off as needed 2 Hold down the Ctrl or Cmd key then click several peaks or clusters
65. 6 e Compound Set Tools on page 100 Remove Selected Compounds If you are certain that you no longer want a compound accessible in Chenomx NMR Suite you can remove it from your library 9 3 Library Tools 99 Enom Menu Location Icon s Hotkey s Library Selected Compounds Remove Delete Delete CHENOMX NMR SUITE USER MANUAL How do remove compounds from my library 1 Selectthe compound that you would like to remove in the Compund Table 2 Click Remove Selected Compounds Tips and Tricks e When you have removed compounds from the library you cannot recover them through Undo If you still have the original compound files xcpd or compound packs pack available you can add them again Related Topics e Compound Table on page 96 e Quick Searches on page 96 e Compound Set Tools on page 100 9 4 Compound Set Tools Compound Sets are groups containing compounds from your library that you can use in Profiler You can create them either by selecting specific compounds Compound Sets or by defining rules for selecting compounds Smart Compound Sets Library Manager includes a number of tools to help you browse and manage compound sets Compound Sets Sidebar The Compound Sets view in the Sidebar contains a list of the currently defined compound sets and lets you interact with them by displaying their contents or editing them The Compound Sets view also contains the Compounds set
66. 9 09 02 Apr 2009 2004 Chenomx Inc Tartrate 800 00 4 23 to 8 86 04May 2009 I 2004 Chenomx Inc i Taurine 800 00 4 05t08 94 27 Mar 2009 2004Chenomx Inc Theophyline 800 00 4 06 to 8 95 24 Apr 2009 2005 Chenomx Inc Threonate 800 00 6 00 to 8 00 04 May 2009 2004 Chenomx Inc Threonine 800 00 4 10 to 9 04 26 Mar 2009 2004 Chenomx Inc Thymidine 800 00 310 08 92 21 Apr 2009 2006 Chenomx Inc Thymine 800 00 4 21 to 9 12 16 Apr 2009 2004 Chenome Inc Thymol 800 00 6 00 to 8 00 05 May 2009 2004 ChenomxInc Tialylolycine 800 00 6 00 to 8 00 05 May 2009 2004Chenomx Inc trans 4 Hydroxy4 proline 800 00 6 00 to 8 00 05 May 2009 2004 Chenomx Inc be trans Aconitate 800 00 4 02 to 9 01 04 May 2009 2004 Chenome Inc l Trigoneline 800 00 4 05 to 9 03 27 Mar 2003 6 2005 Chenomx Inc P Trimethylamine 800 00 4 00 to 8 86 03 Apr 2009 2004 Chenomx Inc Trimethylamine N oxide 800 00 4 03 to 8 78 04 May 2009 2004 Chenomx Inc Tropate mu 800 00 4 09 to 8 80 24 Apr 2009 2006 Chenomx Inc T 297 compounds Compound Sets Sidebar view letting you control which compound set appears in the Compound Table Compound Table Displays information about compounds and their status in the library You can send the signature of a compound to Compound Builder for editing by clicking File Send to Compound Builder or by double clicking on the compound Quick Se
67. 98 new 101 102 remove 103 remove compound from 101 rename 103 sidebar 18 59 100 smart 100 102 103 concentration clear 52 export profiled data 60 exported data txt 31 maximum 56 scale 57 set to maximum 56 units 66 convert automatic 41 multiple spectra 41 settings 41 spectra 41 copy spectrum image to clipboard 24 coupled split 73 creatinine 4 8 32 CSI DSS 4 8 31 editor 31 find automatically 31 formate 4 8 31 internal standard 4 preserve area 31 TSP 4 8 31 custom color 17 46 48 D data acquisition 5 NMR parameters 5 see also NMR parameters pulse sequence 5 datdir 6 default file folder 25 transform window 86 default layout see export delete J modifier 73 75 peak 83 spin definition 71 spin system 70 Delta 5 156 Enom DFTMP 4 8 32 display options sidebar 24 spectrum thumbnail 24 subtraction line 118 sum line 119 X scale 24 Y scale 24 DSS see CSI DSS TSP satellites 39 E edit J modifier 73 75 peak 83 smart compound set 102 spin definition 71 transform window 86 encapsulated PostScript eps 23 enforce transform windows 53 55 exclude region 62 export colors 60 compound files xcpd 98 compound pack pack 98 compound set 98 concentrations 60 data 31 default layout 60 image options 23 matched clusters 60 pins 60 profiled compounds 61 profiled data 60 spectrum image 23 stars 60 transform sum
68. A IA AAN V V M n T T 4 00 3 95 3 90 Figure 10 4 Using frequency filters and sorting by maximum concentration lets you identify serine glycolate and pantothenate as candidate compounds Visual comparison of the signatures to the spectrum line confirms the identifications 10 4 Targeted Profiling 119 CHENOMX NMR SUITE USER MANUAL Compound Lines Sum Line Blue Serine Serine 968 uM Green Glycolate Glycolate 704 uM Purple Pantothenate Pantothenate 104 uM T T T T T T 4 00 3 95 3 90 4 00 3 95 3 90 Figure 10 5 Profiling each compound individually using the basic method simple match to spectrum line yields reasonable concentrations but the sum line doesn t quite match Compound Lines Sum Line Blue Serine Serine 928 uM 4 196 Green Glycolate Glycolate 691 uM 1 9 Purple Pantothenate Pantothenate 82 uM 21 1 T T T T T T 4 00 3 95 3 90 4 00 3 95 3 90 Figure 10 6 Considering all the compounds together along with confirmation using other clusters of serine and pantothenate gives a better match Also note the more than 20 change in pantothenate concentration Water Suppression Spectra of aqueous samples are often acquired using a water suppressing pulse sequence since the water signal would otherwise drown out many useful signals The water suppression pulse can also partially suppress other resonances occurring near the frequency of the
69. Accept button to apply your changes or click the Cancel button to discard them Tips and Tricks You must save the spectrum to retain changes that you have made to the spectrum comments You can only change the CSI settings and spectrum pH using the CSI and pH editors The value ofthe Frequency Domain Size field is set by the amount of zero filling that you select when you convert a spectrum If you selected Automatic the frequency domain size will be the nearest power of two that is at least twice the time domain size Related Topics e Chapter 2 Handling Samples and Spectra on page 4 Importing Spectra on page 13 e CSI Editor on page 31 e pH Editor on page 32 Processing History Sidebar Processing spectra in Processor does not alter your original spectral data Every processing effect that you add to a spectrum acts as a layer modifying the display of your original data All of these effects are completely reversible and are tracked in the Processing History Sidebar view While processing a spectrum you may want to review the processing layers that you have already applied or you may need to reverse the effects of one or more ofthe layers that you have already applied The Processing History maintains a list of every processing layer 5 3 Information Tools 34 Enom Menu Location Icon s Hotkey s View gt Sidebar gt Processing History v Ctrl Shift H Cmd Shift H CHENOMX NMR SUITE
70. Color column and click Clear Icon s g Custom Color Tips and Tricks e Youcanalso set or clear custom colors for compounds visible in the Legend by clicking on the colored box beside the compound in the Legend e Setting a custom color for a compound adds it to the Profiled Compounds set even if you have not set concentrations or transforms for the compound e Custom colors are stored with the spectrum when you save it as a cnx file The colors you select are still associated with the compounds when you next open the file until you clear them 6 3 Profiling Tools 48 evomx CHENOMX NMR SUITE USER MANUAL You can export custom colors to a file using Export Profiled Data Related Topics Legend on page 17 Preferences on page 25 Compound Table on page 46 Pinned Compounds on page 49 Starred Compounds on page 50 Legend Sidebar on page 64 Pinned Compounds It is often useful to display several different compounds at the same time while profiling especially when you are working in heavily overlapped area Pinning a compound ensures that it remains visible regardless of which compound you have selected in the Compound Table In combination with custom colors and exporting spectrum graphics pinning can also help you to prepare snapshots of your profile that are suitable for publication How do I pin a compound Click the pin for the compound in the Pinned column F of the
71. Compound Set Tools on page 59 Transform Windows on page 86 Fit Automatically Profiling a spectrum manually involves a lot of effort in setting initial concentrations and transforms You can have Profiler suggest a concentration and transforms for the currently selected compound allowing you to focus your efforts on tasks like refining your overall analysis of the spectrum or resolving overlapped compounds How do fit a compound automatically Compound Selected 1 Menu Location j Compound gt Fit Automatically Select the compound in the Compound Table If you do not see the compound in the Compound Table select additional compound sets or use Quick Searches to find 2 On the Compound menu click Selected Compound gt Fit Automatically or right click on the compound and select Fit Automatically from the context menu Tips and Tricks e Although Profiler will often arrive at acceptable values always review the results of an automatic fit before moving on to other compounds e Fit Automatically yields more reliable results from properly processed spectra This includes well defined CSI parameters and accurate spectrum pH values Related Topics e CSI Editor on page 31 e pH Editor on page 32 e Concentrations on page 52 e Transforms on page 53 Enforce Transform Windows Transform windows appear in compound signatures to guide profiling by restricting the amount that you can transform e
72. Compound Set that you would like the compound to appear in If you would not like to automatically add the compound to a new Compound Set clear the check box 7 Click Finish and click OK in the resulting information dialog If you created a Compound Set it appears in the Compound Set Table Otherwise you can find your newly added compounds in the Compounds set at the top of the Compound Set Table You can use the same method to add compound packs that you may receive from other Chenomx NMR Suite users to your library Simply select one or more compound pack files pack instead of selecting individual compound files You can even select a folder containing a mixture of compound files xcpd compound packs pack and legacy files containing library information cnx and cnxlib to import from a variety of sources at the same time 10 9 Using Expressions Building advanced compound signatures in Compound Builder may involve using mathematical expressions to set peak centers heights or widths or cluster transform windows Text fields in which mathematical expressions are allowed contain a button indicating that expressions are supported for the field You can click the button to open a simple expression editor useful for editing more complicated multiline expressions Numbers that you enter in expressions must be in US English style decimal notation e g 6 4378 or 12 038203 or US computerized scientific notation e g 2
73. Compound Table you can click its shape inthe Spectrum View then use the W and S keys or up and down arrow keys to adjust its concentration up and down Hold down Shift to allow finer adjustments 6 3 Profiling Tools 52 evomx CHENOMX NMR SUITE USER MANUAL Once you have set a concentration for a compound it appears in the Profiled Compounds set Selecting that set shows only compounds that you have profiled in the Compound Table You can hover the mouse cursor over any cluster or its transform adjustment triangle on the horizontal axis or the compound s concentration adjustment triangle on the vertical axis to see the concentration for the current compound even when the Concentration column is not visible in the Compound Table The concentration appears in the top right corner of the Spectrum View To clear all of the concentrations for the current spectrum select Compound gt All Compounds gt Clear Concentrations To clear concentrations only for starred compounds select Compound gt Starred Compounds gt Clear Concentrations All compound concentrations start out as unknown Ifacompound s concentration is unknown and you dragit up and then back down to the baseline the concentration is set to 0 00 mM To return the concentration to unknown you must clear it When you Export Profiled Data compounds with unknown concentrations are not exported unless other spectra in the exported set have those comp
74. Concentrations Once you have identified compounds present in a sample you need to determine their concentrations based on the data inthe spectrum If you have automatically fita compound you may need to refine the suggested concentration For more details on techniques for determining optimal profiles for compounds in experimental spectra see Targeted Profiling on page 116 3 4 Profiling Overlapped Regions in a Spectrum 11 CHENOMX NMR SUITE USER MANUAL To determine the concentration of a compound 1 If the subtraction line green is not currently visible turn it on see Legend on page 17 Set a concentration for the compound so that you can see the clusters clearly see Concentrations on page 52 Use the Cluster Navigator to locate a cluster that you can use to approximate the compound concentration see Cluster Navigator on page 58 When choosing a cluster with which to establish a compound s concentration use a cluster that overlaps other clusters as little as possible Click and drag the height control for the compound and observe the subtraction line Adjust the height of the compound until the subtraction line under the cluster approximates a normal spectrum You may need to move transform the cluster side to side somewhat to properly adjust the subtraction line see Subtraction Line on page 118 Concentrations on page 52 and Transforms on page 53 If any of the cluste
75. Enom CHENOMX NMR SUITE USER MANUAL How do I set starred compounds to their maximum concentrations Compound gt Starred Menu Location Compounds gt Set to Maximum Concentrations Icon s Ni 1 Staratleastone compound 2 Onthe Compound menu click Starred Compounds Set to Maximum Concentrations How do I set all compounds to their maximum concentrations 1 OntheCompound menu click All Compounds gt Set to Maximum Concentrations Compound gt All Compounds gt Menu Location x s Setto Maximum Concentrations Icon s Ni Tips and Tricks e Maximum concentrations in Profiler refer to estimates that are subject to error based on assumptions that may not coincide with your interpretation ofthe spectrum Verify any results that you obtain based on maximum concentrations The method used to determine maximum concentrations is simpler than that used for automatic fits Concentrations calculated by the two methods may differ Related Topics e Compound Table on page 46 e Starred Compounds on page 50 e Quick Searches on page 50 e Concentrations on page 52 e Fit Automatically on page 55 e Compound Set Tools on page 100 Scale Concentrations Scale Concentrations lets you modify the concentrations of all profiled compounds in the current spectrum by a common multiplication factor You can use this to compensate for dilution effects errors in CSI concentration or other
76. IE RR bDUK 77 8 1 OVETV EW 77 8 2 Quick Reference Guide siirus iiisi iieri iiin nennen nennen Eiaeia i E nnn 78 8 3 Building TOONS inneni aroni OA A 80 avance 80 Import Simulation rossii 9 3 5 a xeSe rei tepsedc sa EEE use sitem a ekE ER EE 80 Lunar new EEUU 81 Selecting Peaks and Clusters ssssssssseeeeemn 82 Delete Selected Peaks eit Laaer Eii 83 Adjusting Peaks ite xecesl ix co d deiode iix Ro ia ux ada Ric MA KRM KR NUS RINE DOS UE 83 Grouping Peaks as a Cluster ssessesesseeen mmm 84 Optimize Selected Peak Shapes sssesseeeeeenmmn 85 Generate Cluster for Region i eet tb E Ee ERE RENE Ex REO TES e rGA 86 ecvioansMon E nniaii 86 pH Sensitivities ecd iisteseiu koe EP Ro ee LLe D ed FER EEAXE ELM Die ENEA ERESSE 88 jENEP CASSEL 90 Cluster NavigatoE ois ER A REFERO ERU eM EI ier KE eM UEERE 90 E Migne 91 Reference Panel Sidebar eee tette et ne eR E 91 Gompound Details P E 91 Information Panel enceinte E rro ER XXE Ea C pU PAY E SUEF IKE 92 9 BincwauENEI Jd E 94 9 1 OVERVICW nnm 94 9 2 Quick Reference Guide cccceccsecsceseceeeecaeeuecaeeseeeeeseeeeeneeeeenesaeeneeaeeneaes 95 9 3 library TOONS etie eH ER REI ter eeu Lied 96 Compound Table SEPT 96 Quick Searched enei Eao E a a eei EE EaR stands 96 Add Compounds sssaaa aE R AE ARRERA 97 Export CompoOUnds
77. In Library Manager opens the compound file xcpd of the selected compound in Compound Builder for modification or review In Profiler opens the current spectrum in Processor to let you modify the processing layers CSI settings spectrum pH or spectrum details The details ofthe current profile concentrations transforms etc are retained even if you then save and close the spectrum from Processor In Processor opens the current spectrum in Profiler to start or continue profiling Any changes to the processing layers CSI setting spectrum pH or spectrum details are retained even ifyou then save and close the spectrum from Profiler See standardized intensity Dedicated area of the screen that displays frequently used information related to the Spectrum View Available views include Compound Sets Profiler Legend all modules except Library Manager Processing History Processor Reference Panel Profiler and Compound Builder and Simulation Spin Simulator A string of characters that uniquely represents a chemical compound based on its structure Developed by David Weininger and extended by Daylight Chemical Information Systems Inc Sidebar view that lets you view and edit spin definition properties and create edit or remove J modifiers In Spin Simulator information about the current simulation including simulation frequency in MHz number of spin systems number of transitions modeled and number of J modifiers
78. InChI or SMILES codes for valine you can enter them here as well 10 6 Compound Builder 129 evomx CHENOMX NMR SUITE USER MANUAL 7 Inthe Advanced tab enter the molecular weight of valine to four decimal places 117 1463 Also enter a valid pH of 6 92 Enter noesy as the pulse sequence 8 ClickOK You will need to set appropriate transform windows before adding the signature to your library However setting the default 0 006 ppm transform windows for all clusters provides an easy way to ensure useful zoom levels when using the Cluster Navigator to move around the spectrum Also turning on the subtraction line can give you valuable insight into how well the compound fits the experimental spectrum 9 Click Compound gt Transform Window gt Set Default on All Clusters to set a default transform window 0 006 ppm wide centered on the cluster center for every cluster in the compound 10 Switch to the Legend sidebar and turn on the subtraction line green Several of the clusters in the imported simulation are quite simple Focus on matching the simple clusters to the spectrum first and then deal with the more complex cluster 11 Moveto the cluster near 3 6 ppm using the Cluster Navigator and select it 12 Adjustthe cluster blue to fit the spectrum black To further refine the shape adjust the cluster so that the subtraction line is as flat as possible When you are adjusting simple clusters you can get a v
79. Linux Windows Mac OS X e pH Sensitivities Ctrl Shift P Cmd Shift P Manage Cluster IDs oe 85 Optimize Selected Peak Shapes Ctrl I Cmd I F Generate Cluster for Region Ctrl Shift I Cmd Shift I Help Menu NMR Suite Help F1 F1 td Save Application Log Ctrl Shift A Cmd Shift A E Software Activation 9 About Chenomx NMR Suite 8 3 Building Tools Compound Builder includes a variety of tools to help you build compound signatures by adding manipulating and removing peaks grouping peaks into clusters and defining ranges within which clusters can move You can also generate arbitrary clusters to match the overall lineshape of a region or optimize peaks to better match the spectrum New Compound New Compound creates a new compound file xcpd The new compound file has the default Compound Details including a magnet frequency of 800 MHz and a sample Menu Location File New Compound S concentration of 5 mM Icon s P Tips and Tricks Ctri N Hotkey s Cmd N e New compound files do not have a spectrum overlay Add a spectrum overlay before you begin build a compound signature You can overlay one spectrum at a time in Compound Builder e You need to save the new file to retain changes that you have made Related Topics e Spectrum Overlays on page 19 e Compound Details on page 91 Import Simulation Importing lets you use an existing spin simulation xss or
80. R SUITE USER MANUAL 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 You can simply click on the sum line red to select the nearest compound Click repeatedly to cycle through the contributing compounds in an overlap region Move to the next pantothenate cluster 3 4 ppm using the Cluster Navigator and adjust the frequency of the cluster at 3 39 ppm to fit the spectrum In the Compound Table and use Fit Automatically on fucose and taurine and then select taurine Move to the taurine cluster near 3 3 ppm and adjust it as needed to match the spectrum Return to the taurine cluster near 3 4 ppm and adjust its frequency as needed to match the spectrum In overlapped regions like this the sum line red becomes a better indicator of the quality of your profile in the region so check the match of the sum line to the spectrum before proceeding Select fucose and use the Cluster Navigator to display the clusters near 1 2 ppm Click and drag across the series of clusters in the Cluster Navigator to view the entire group Adjust the concentration of fucose so that the clusters near 1 2 ppm match the spectrum The cluster at 1 24 ppm provides the best reference to establish the concentration for fucose Return to the fucose cluster near 3 4 ppm and adjust its frequency as needed to match the spectrum using the sum line to evaluate your progress Select pantothenate again an
81. R Suite that lets you prepare and modify spin simulations xss Grouping of spin definitions in Spin Simulator that are uncoupled to any other spin definitions Chemically a spin system corresponds to a group of protons in a compound that do not interact with any other protons in the compound in a manner detectable by NMR 152 Enom CHENOMX NMR SUITE USER MANUAL spline split count standardized area standardized intensity standardized width starred compound subtraction line subtraction line fit sum line sum line fit SVg A curved line formed by two or more vertices or breakpoints and a mathematical formula that describes the curves between them One of the two parameters that define a J modifier For coupled splits the split count is predefined as the number of protons associated with the spin definition to which the current spin definition is coupled For uncoupled splits you may consider the split count as the number of virtual protons to which the spin definition would need to be coupled to show the desired splitting pattern Refers to an area relative to that of a theoretical DSS methyl peak at a concentration of 0 50 millimoles per litre mM Refers to an intensity relative to that of a theoretical DSS methyl peak at a concentration of 0 50 millimoles per litre mM Using this scale if you select DSS as your CSI and indicate a DSS concentration of 1 00 mM then the intensity of the DSS me
82. TE USER MANUAL evomx T targeted binning targeted profiling text filter time domain size TMSP transform transform summaries transform window transitions TSP uncoupled split universally unique identifier Variation of spectral binning in which the bins are defined as the transform windows of each cluster of each compound ina compound set Data reduction method embodied in the Profiler module involving comparing a spectrum to compound signatures in your Library thus reducing spectral data to a list of quantified compounds A quick search based on entered text Filters the Compound Table by matching compound name compound comment compound ID or location in the spectrum Profiler only in ppm The number of data points originally acquired for a spectrum if it originated from a raw fid or the number of points originally saved in a spectrum if it was processed using a third party software package See TSP Translation ofa cluster in a compound signature along the frequency axis during profiling Transforms are necessary to compensate for variation in cluster frequency due to pH ionic strength and other matrix effects In Profiler values for profiled compounds indicating whether clusters for each compound are within their respective transform windows or outside them May be exported using Export Profiled Data Limit placed on the extent of transforms possible on a particular cluster Lo
83. XUJOUSUO Chenomx NMR Suite 7 0 Copyright O 2001 2010 Chenomx Inc CHENOMX NMR SUITE USER MANUAL Table of Contents Notices and Trademarks oer eter n a XE exe n RN Ea vii Ly INtFOCUCHION p S 1 I PMECIEMIPE EUER 1 Windows 32 bit itti pnta epeke keep eisut a cene ceb pst d Pus dR vr E PAM 1 Windows 64 bit scsi eere UP E E eM FER E E REREEPUM 1 Mac OS E 1 Linux 32 bit 2 5 eoe E E 1 Ier 0i R 2 1 2 Activation and Licensing iier onc Ghani Deere ER ERE SME Meere R ERES 2 1 3 Adding the Chenomx Reference Compounds eeseseeeeee 3 2 Handling Samples and Spectra ssssssessesessseeeene meme nennen 4 2 1 Sample Pr paration cniin rcise ede insi eines edsc i pieqi adada Pu oPIS E reds 4 Internal Standard Solution eite teo ri enti ho ote in oae x A TRE Ere ne IE 4 2 2 Spectral Data Acquisition wes sitecccsaicd cedes n oia Rec p ni S aA EAEE E EE 5 Pulse Seque nc s 2 ti mete iR cu m RUE tress 5 Required NMR Parameters ccceeeeeeeeeeeeeeeee ee ee tesa ee ae cena eee ee Ekoa eni 5 2 3 Spectral Data Processing ceo SEHE UE Ee Mii Ex EUM a t TERRE A 5 Data Processed with Other Software ssesseee em 6 3 Common Tasks t epit etx aL Eos kr ERR x Ian PE bk da wnanusasdaveadsaveindbssaaindtaaeesmants 8 3 1 Processing a Spectr m o csi ccscsccswedeccsdsanis coecteccectsenadcdtendeetsdcoanecdeatnec
84. a PF m In the Compound Table select the compound with the highest Maximum Concentration acetate as this is the most likely candidate for fitting the peak You may want to sort the Compound Table by Maximum Concentration to make selecting the highest Maximum Concentration simpler Click the header of the Maximum Concentration column to sort by that column Additional clicks on the header reverse the sort order 6 Click Compound gt Selected Compound gt Fit Automatically or press the space bar Profiler s automatic fit suggests concentrations and transforms for the currently selected compound Although it will often arrive at acceptable values always review the results of an automatic fit before moving on to other compounds 7 Adjust the acetate signature blue as needed to match it to the corresponding peak in the spectrum black You can click and drag the controls on the horizontal and vertical axes to move the peak along only one axis at a time or use the arrow keys to move the peak up down left and right 8 Clear the quick search box above the Compound Table by clicking the red X or pressing Esc 9 Click Show Entire Spectrum Single Peak Compound Pyruvate 10 Zoom in on the single peak near 2 40 ppm 10 3 Profiler 110 evomx CHENOMX NMR SUITE USER MANUAL 11 12 13 14 15 16 Right click on the peak and click Filter for Compounds Near 2 36 ppm In the Compound Table select p
85. able in Spin Simulator as well as with the basic process involved in creating a simulation you will simulate a simple compound valine 10 5 Spin Simulator 122 nom CHENOMX NMR SUITE USER MANUAL 1 d 4 A x3 H3C i NH Aside from exchangeable protons like the carboxylic acid and amine protons there are four types of protons expected to have visible signals for this compound marked as 1 through 4 in the structure above The two methyl groups 1 and 2 and one of the methine groups 3 will each couple to the remaining methine group 4 Thus in the spectrum for valine you would expect to see three doublets each coupled to one complex cluster rigorously a quartet of quartets of doublets or qqd OH Simulating Valine 1 Assignthe spectrum matching protons in the structure ofthe compound with signals in the spectrum For valine the assignments are as follows a Methylsignals 1 and 2 appear at 0 978 and 1 031 each coupled to one ofthe the methine signals 4 b Methine signal 3 appears at 3 604 ppm and is coupled to the other methine 4 c Methine signal 4 appears at 2 264 ppm and is coupled to each of the other three signals 2 OpenSpin Simulator 3 Overlay the valine spectrum called Samples Spin Simulator NValine cnx 4 Add spin definitions for each ofthe signals from the assignment above starting from the right hand side of the spectrum low numbers and moving left to higher numbers
86. ach cluster All Chenomx Reference Compounds have had transform windows set to allow the flexibility to fit most common biofluids You can choose to have the transform windows enforced preventing you from moving any cluster outside its transform window or not enforced allowing you to move any cluster beyond its transform window 6 3 Profiling Tools 55 evomx CHENOMX NMR SUITE USER MANUAL How do I enforce transform windows Menu Location Hotkey s Edit Enforce Transform Windows Ctrl Shift X Cmd Shift X 1 On the Edit menu check Enforce Transform Windows How do I allow clusters to move outside their transform windows 1 On the Edit menu clear Enforce Transform Windows Tips and Tricks Clusters that are outside their transform window appear in the Transforms column of the Compound Table as Outside Windows Note that you may need to turn on the Transforms column in the Compound Table When you transform a cluster outside its transform window its transform adjustment triangle turns red Also when you hover over the cluster or its triangle the visual indicator for the transform is red as is the text in the top right corner of the Spectrum View describing the extent of the transform Transform windows for pH sensitive compound signatures are determined in part based on the pH uncertainty for the current spectrum If you find that you frequently need to override the transform windows for a spectru
87. aeactanaeeneacesy 117 10 5 Spin Simulator ertet ree EI EPI RR DRM M exei eerste 122 liviadesiitent rgeet rr 122 Simple Simulation Valine ssssssee en 122 Complex Simulation Proline ssseseeenm m 125 10 6 Compound Bullder br tpe rx eo E eo RAUS ERE XR cence 128 Jtrod ctiOn creci er 128 Simple Compound Valine sssrinin i mm meme 129 Complex Compound Proline seseeeeenm mm 131 10 7 Building pH Sensitive Compounds esseeeeeeee 133 Introduction pe HR 133 Building a pH Sensitive Compound ssseeeeeeeeee 133 10 8 Library Manager 5 titius fees ecdsneick cda eoxu Ie sda o deco orx ocu dos eRo ed ar 134 Introducti OM e EUM 134 Adding Compound retta std saxea cusan aa avorscaiaeccivetvacosaaducces 134 10 9 Using Expressions entree Hee tea Foxit M E Miisarixei Ae ec e nbEEKUE 135 Chemistry Related Expressions ssssseeenm 138 Glossary innean ana e e emitir REM d ERI ELI tee ele ete 141 ll 156 vi evomx Menu Location Icon s Hotkey s Help gt Save Application Log bd Ctrl Shift A Cmd Shift A CHENOMX NMR SUITE USER MANUAL Notices and Trademarks Developed by Chenomx Inc 2001 2010 Chenomx Inc No copying or reproduction allowed without express written permission T
88. age to Clipboard 24 CHENOMX NMR SUITE USER MANUAL Sidebar Simulation Show Sidebar Show Spectrum Thumbnail Switches the Sidebar to the Simulation view Available in Spin Simulator Toggles the display ofthe Sidebar Available in every module except Library Manager Toggles the display ofthe spectrum thumbnail in modules with a Spectrum View Tips and Tricks e You can change the colors of the various graph elements noted above as well as that ofthe background and zoom box in the Preferences for the appropriate module Related Topics e Preferences on page 25 4 14 Preferences In Preferences you can specify default folders default settings for the Spectrum View colors of various graph elements and some module specific settings Menu Location Icon s File Preferences How do I change preferences 1 Openthe Preferences module 2 Selectthe module for which you would like to change preferences 3 Make your desired changes 4 ClickOK How do I use a proxy server with Chenomx NMR Suite 1 Switch to the General module in Preferences 2 Inthe Internet Preferences section select Proxy connection to the Internet 3 Enterthe IP address of your proxy server and the port that Chenomx NMR Suite should use to access it How do turn off animated zooming 1 Switch to the General module in Preferences 2 Clearthe check box labeled Enable Zoom Animation How do I
89. al Delete the water peak from the spectrum see Water Deletion on page 40 Water deletion may not be necessary or desirable for all samples Save the spectrum see Saving Files on page 14 or jump to Profiler see Chapter 6 Profiler on page 43 to continue with your analysis 3 2 Profiling a Spectrum Profiling a spectrum using targeted profiling is a very flexible task You can vary the number of compounds profiled in a particular spectrum to suit a variety of timeframes research goals or other requirements One ofthe most important aspects of your approach to profiling a spectrum should be maintaining a consistent profiling strategy as this gives you more consistent and more easily interpreted results For more details on specific profiling techniques and how to apply them to your spectra please see Targeted Profiling on page 116 3 1 Processing a Spectrum 8 evomx CHENOMX NMR SUITE USER MANUAL To profile a spectrum using targeted profiling 1 Process the spectrum see Processing a Spectrum on page 8 2 Optional Create a compound set containing the compounds that you would like to analyze see Compound Set Tools on page 100 3 Open the spectrum in Profiler see Opening Files on page 13 4 Select a compound set containing compounds appropriate for the sample If you created a compound set above select the compound set that you created 5 Identify and profile prominent signals
90. an asymmetric baseline on either side of peaks and peak clusters in the spectrum In some cases you may see whole peaks inverted pointing down from the baseline instead of up while extreme phase shifts may also add a periodic oscillation or rolling to the baseline Most spectra require some degree of phase correction Adjust phasing before applying any other processing layers to your spectrum like baseline correction or reference deconvolution While importing a spectrum you may choose to have Processor automatically apply phasing adjustments After importing a spectrum you can apply automatic or manual phase correction In either case a Phasing layer appears in the Processing History you can remove the layer if necessary How do apply phase correction to my spectrum Menu Location Icon s Hotkey s Processing Phasing pot Ctrl Alt 1 Cmd Alt 1 1 2 Switch to Phasing mode Automatic Click the Auto button to have Processor automatically calculate phase angles Review the spectrum after automatic phasing to ensure that the results are acceptable If necessary you can use the manual controls to adjust the phase angles before accepting them Manual Click and drag the Zero order Phase and First order Phase sliders or type angles in the boxes beside each slider Use the Normal Fine or Very Fine modes to select the scale of changes made with the sliders Click the Accept button to apply your changes or
91. applying it consistently to all spectra in a dataset profiling can involve a variety of methods depending on the intensity of the peaks the presence of other peaks in the region the degree of overlap with other peaks and the presence of other clusters from the same compound elsewhere in the spectrum Some ofthese methods are described below you may discover other methods as you analyze more spectra These techniques refer specifically to manual profiling as well as refining the results of automatic fits using Fit Automatically Identifying Compounds There are a variety of methods that you can use to help you identify compounds that are presentinany given spectrum Some are implemented directly in the Profiler module while others may involve some literature review or external reference Each of the following techniques is essentially a method of limiting the list of potential compounds for a given region of the spectrum You must make the final decision as to whether or not a particular compound is represented in the spectrum by visually comparing the signature for the compound to the patterns visible in the spectrum Remember that each cluster can be moved somewhat to either side of its starting position inside its transform window and the overall height of the compound can be adjusted Frequency Filters You can use Filter Compounds to filter the Compound Table to include only compounds that can appear at a certain frequency or in a
92. arch Lets you filter the Compound Table to focus on a particular compound or group of compounds Status Bar Displays information about recent user actions 9 1 Overview 94 evomx CHENOMX NMR SUITE USER MANUAL 9 2 Quick Reference Guide Linux Windows Mac OS X File Menu D New Compound Set Ctrl N Cmd N D New Smart Compound Set Ctrl Shift N Cmd Shift N D Edit Smart Compound Set Ctrl E Cmd E D Rename Compound Set Ctrl R Cmd R IR Remove Compound Set Delete Delete A Send to Compound Builder Ctrl J Cmd J Preferences px Exit eae Edit Menu V Undo Ctrl Z Cmd Z Redo Ctrl Y Cmd Y Select All Ctrl A Cmd A View Menu EM Change Columns Library Menu Add Compounds Selected Compounds Submenu a Add to Compound Set F Remove Delete Delete Export to gt Compound Pack pack eem Export to gt Compound Files xcpd pum ees Help Menu NMR Suite Help F1 F1 td Save Application Log Ctrl Shift A Cmd Shift A Software Activation 9 About Chenomx NMR Suite 9 2 Quick Reference Guide 95 CHENOMX NMR SUITE USER MANUAL 9 3 Library Tools Library Manager lets you browse and manage the contents of your library Your library contains all of the compounds that you can use to profile a spectrum at all magnet frequencies pH ranges and pulse sequences Compound Table The Compound Table in Lib
93. are profiling a series of spectra from the same study the spectra are often quite similar to one another While it is possible to profile each spectrum from scratch it can be more efficient to copy a profile from an earlier spectrum in the series and adjust itto match the current spectrum Importing profiles is an important technique for profiling large series of similar spectra efficiently How do import a profile from another spectrum 1 Openthe Import Profile dialog 2 Selecta profiled spectrum cnx from which you would like to import the profile 3 Click Import Tips and Tricks e When you import a profile the imported data completely replaces any profile of the current spectrum that you may have done before the import Related Topics e Profiling Tools on page 46 Spectral Binning Statistical approaches to analyzing large numbers of spectra often involve data reduction methods like spectral binning to reduce the number of variables that must be considered Spectral binning divides spectra into a series ofregions or bins subsequent analysis involves the integrated area of these bins instead of the raw spectral data Profiler lets you perform spectral binning on collections of spectra exporting the results to a text file format that is easily read by spreadsheet programs and statistical analysis software packages How do I bin spectra 1 Startthe Spectral Binning wizard 2 Choose the source spectra cnx for binn
94. arily limit the number of compounds appearing in the Compound Table based on search criteria The search criteria can include text searches based on compound name location compound IDs compound comments or all of these You can also search by frequency listing all compounds appearing at a specific frequency or within a range of frequencies How do I limit the compounds visible in the Compound Table 1 Click the binoculars icon at the left edge of the search box to choose the type of search to use Compound Name Compound Comment Compound ID Location or All If you do not specify a search type the default is All 6 3 Profiling Tools 50 evxomx CHENOMX NMR SUITE USER MANUAL Type your search terms in the Quick Search box at the top left of the Compound Table The contents of the Compound Table update to show all matches to your current entry Click the red X at the right edge of the search box to cancel the search and restore the full list of compounds Clearing the search field also resets the search type to All How do search for compounds near a single frequency using the Spectrum View 1 2 Right click on the spectrum and click Filter for Compounds Near x xx ppm Click the red X at the right edge of the search box to cancel the search and restore the full list of compounds How do search for compounds in a frequency range using a selected region 1 2 Use the Select Region tool to select a region of
95. arsdsieendsndegadusdianons 59 6 5 Importing and Exporting Data ssesseseseseee mmm 60 Export Profiled Data sirisser nnna aoii 60 Export Profiled Compounds 0 cccececeeeee ee ee eect ee eee ee eee mener 61 opfjadeg t D M U m 62 Spectra Binning vse Due pte ineix Da ae area Serihuus 62 Send to PROCESSOR Pe M M 64 6 6 Information To0ls etie tr ERE EIE EUR Ex e ERE EPARE ER eie Re RN 64 Legend Sidebar itte vaceudend E EAEE 64 Reference Panel Sidebar ccccceeeeeeeee eect eee ce E ANE EE 65 Spectrum Details siscccsieceesccsnadecctgctenscadacdecesdangssageieestasemnseaesedeanacuancaaca 65 Concentration UNIES ee riketeesiu esee dto cheatin Eh aE EEEE 66 ODESlEL E NEP 67 7A OVETVIEW MEM 67 7 2 Quick Reference Guide ccccccsececesecaeeeecaeeeecaeeesaeeneeeeeneseeeneseseneeaeegenn ees 68 CHENOMX NMR SUITE USER MANUAL VESSEXIUIEDBIPAINUEEEUEEMM 70 New Simulation etes te Pea E EAS FEE RE TR TAX EEN EE EEEE EE 70 KIEL 70 SuSE m 71 Spin NaVigator as cisccccccce nsei neinet canna chant endecestues cinawensns comes ed 73 J ModifietS icio reo rotor erra EEEE EE EATON E EEA 73 7 4 Information Tools esee bano traer pr etre saaea i xoci nae eua Ax sd Eois 75 Simulation Sidebar ione te m ERR ME eot e EI 75 invicem T 76 8 Compound Builder 3 Ee nere ben A PR RESI ELE
96. at would you like to export You can export concentrations in various units other profiling results like matched clusters and transform summaries or annotations like stars pins and custom colors Choose the compounds for which you would like to export data You can use custom compound sets that you have created in Library Manager to filter the output to specific compounds or you can export all profiled compounds in all ofthe spectra Choose additional data that you would like to include in the exported file Additional data can include spectrum pH values Chenomx compound IDs for the exported compounds or InChI or SMILES strings for the exported compounds Choose the default layout files in rows and compounds in columns or transposed layout compounds in rows files in columns for the output file depending on how you intend to use the file Tips and Tricks If you do not explicitly specify a target file and folder an appropriately named file is created in the folder containing your source spectra Possible file names include e concentrations txt e matched clusters txt e transform summaries txt e stars txt e pins txt e colors txt 6 5 Importing and Exporting Data 60 Enom CHENOMX NMR SUITE USER MANUAL To filter the exported compounds without modifying the source spectra create a Compound Set or Smart Compound Set in Library Manager and only export compounds in your custom Compound Set To set spectrum pH value
97. at you have made Related Topics e Spectrum Overlays on page 19 e Simulation Details on page 76 Spin Systems If you need to model many protons in a simulation you may want to use spin systems to organize them A spin system in Spin Simulator is a set of spin definitions that you have defined as only interacting with other spin definitions within the set Chemically this may be loosely interpreted as a set of protons that couple only to each other 7 3 Simulating Tools 70 CHENOMX NMR SUITE USER MANUAL How do I add a new spin system Menu Location ens end New Spin 1 Click Add New Spin System ystem Icon s 2 Ifthis is the first spin system you have added a new dropdown list appears in the Simulation view above the Spin Definition Tabs listing the available spin systems Additional spin systems also appear in this dropdown list How do I select a different spin system 1 IntheSimulation view select the spin system to which you would like to switch from the drop down list Alternately select a spin definition belonging to the other spin system in the Spectrum View How do I delete a spin system Menu Location Simulation i ae ae 1 Select a spin system from the drop down list in the Simulation view EE X 2 Click Delete Current Spin System Tips and Tricks e Deleting a spin system deletes all spin definitions and J modifiers associated with the spin system as well Related
98. ately half height to adjust their widths e Use the W and S keys or the up and down arrow keys to adjust the height of the selection up and down e Use the A and D keys or the left and right arrow keys to adjust the position of the selection left and right e Use the Q and E keys to display the next or previous cluster Tips and Tricks When you enter specific amplitudes and widths in the Edit Selected Peaks dialog all of the selected peaks are set to the specified values regardless of which clusters they are associated with When you enter a new center in the Edit Selected Peaks dialog the geometric center of the selected peaks becomes the value that you entered Double click on a peak or cluster in the Information Panel to open the Edit Selected Peaks dialog for the double clicked item Right click on a selection in the Spectrum View or Information Panel and select Edit Selected Peaks to edit properties for the selection When you adjust the properties for a single peak you can use mathematical expressions instead of single values to set the center height and width of the peak To insert an expression instead of a single value right click in the text box that you would like to change then click Expression To view or edit an existing expression click the expression icon in the text box that you would like to change Related Topics Add Peak on page 81 Selecting Peaks and Clusters on page 82 Grouping Peaks a
99. automatically determined breakpoints Remove the water region from the spectrum during the import process Reverse Spectrum Bruker only Reverse your spectrum horizontally Only available when you import Bruker spectrum files fid Saving a file ensures that any changes you have made are preserved for future reference When you are working on a complex task save often 4 3 Saving Files 14 CHENOMX NMR SUITE USER MANUAL How do I save a file Menu Location File gt Save Save As 1 Click Save i x m 1 con s H 2 Ifyou have not previously specified a location and filename do so now Ctrl S Hotkey s How do I save a file with a different file name 1 ClickSave As 2 Locate the folder in which you would like to save the spectrum 3 IntheFile Name field type the new name of the spectrum file 4 Click Save Tips and Tricks e Saving compound files in Compound Builder or simulation files in Spin Simulator preserves only the mathematical peak descriptions created during the fitting process Compound Builder and Spin Simulator do not retain spectrum overlays in the saved files 4 4 Closing Files When you finish working with a file you can close it and open a new one without exiting the program How do I close a file Menu Location File Close 1 Click Close kan U 2 Ifyou have made changes to the file and they are not saved choose whether you Ctrl W would like to save the chang
100. axis in the Spectrum View If the compound already has a concentration set you can click and drag any cluster horizontally to change its transform How do I clear transforms for a compound 1 Select a transformed compound in the Compound Table If you do not see any transformed compounds in the Compound Table make sure the Profiled Compounds setis selected If you still do not see any transformed compounds then the current file may not contain any transformed compounds In the Compound menu click Selected gt Clear Transform or right click on the compound in the Spectrum View or the Compound Table and click Clear Transform The compound s clusters return to their default locations Tips and Tricks You can have Profiler suggest concentration and transform values for the currently selected compound by clicking Compound gt Selected Compound gt Fit Automatically or by pressing the space bar When you have selected a compound in the Compound Table you can click one of its clusters in the Spectrum View then use the left and right arrow keys to adjust the cluster s transform Hold down Shift to allow finer adjustments If the transform window does not allow you to move a cluster far enough to fit your spectrum you can disable enforcement of the transform windows by clicking Edit gt Enforce Transform Windows You can hover the mouse cursor over any cluster or its transform adjustment triangle on the horizontal axis to see the
101. ble lines including the spectrum spectrum overlay sum compound simulation subtraction CSI and pinned lines where applicable Processing layer available in Processor Also the process of compensating for distortions in the non signal noise regions of a spectrum Simple profiling technique involving small transforms of indistinct clusters to yield an aesthetic improvement in the profile in the absence of concrete information on which to base a more accurate approach 141 evomx CHENOMX NMR SUITE USER MANUAL bin Bruker processed spectrum data chemical shift and shape indicator chemical shift equivalent Chenomx compound ID Chenomx Reference Compounds cluster Cluster Navigator cnx cnxlic Compound Builder compound details compound file In spectral binning a region ofthe source spectrum that has been reduced to a single value representing the area under the curve in that region Processed Fourier transformed data from spectra acquired using Bruker spectrometers and processed using the XWIN NMR software package developed by Bruker Refers to a signal in the spectrum used to calibrate the chemical shifts lineshapes and concentrations of compounds in your Library Also refers to the compound responsible for the signal Describes a relationship within a molecule between nuclei that are interchangeable by symmetry operations or by a rapid process Arbitrary positive integer assign
102. center is 0 9781524039197456 when the spectrum pH ph is 6 92 Transform Window The transform window operation performs the cluster center operation described above at several pH values and uses the results to determine error bounds for the computed center ofthe modeled cluster In effect it computes the cluster s transform window Transform windows are based on the underlying assumption that there is always an error in any pH value passed into the clusterCenter operation termed errorPh Since a cluster s center moves primarily with pH errorPh can then be used to represent a boundary on the amount of error in our overall cluster center calculations More specifically upper and lower error bounds are determined for the cluster center by recalculating the cluster center at ph phError and ph phError Ifthe cluster center function has any local extrema that fall within that range the cluster center at each extremum is also calculated The extrema must be provided as parameters to the transform window operation see the example below 10 9 Using Expressions 138 evomx CHENOMX NMR SUITE USER MANUAL The transform window operation returns either the highest or lowest of all the computed centers depending on whether or not the upper parameter is set to true You can also set a minDeltaPPM parameter which ensures that the returned boundary is a least aminimum distance away from the unmodified clusterCenter value This is useful fo
103. change colors 1 Click the swatch box corresponding to the color you would like to change 2 Clicka new color on the color palette 3 Click OK to accept the selected color How do I set the initial zoom 1 Selecta module tab 2 Selectthe Initial Zoom check box 3 In the Initial Zoom fields enter the default values in ppm for the range ofthe spectrum to display 4 14 Preferences 25 Enom CHENOMX NMR SUITE USER MANUAL How do I specify the default file folder 1 2 3 4 5 Select a module tab Click the Always use this folder button Click the default folder browse button Locate the desired folder Click Select to select the specified folder Tips and Tricks When you click on a color swatch to change a color the simple color chooser that appears initially lets you choose from a selection of 15 common well distinguished colors Colors in this selection that are already used in the current module s preferences are indicated with a faint white checkmark while the currently selected color is indicated with a strong white checkmark When you change a color in Preferences you are setting a new default color meaning that the element whose color you set will appear in that color every time you use Chenomx NMR Suite Avoid light line colors with a light or white background as they are difficult to see on screen or in a printout The low and high frequencies for the initial zoom must be atleast 1
104. cinamide 581 4 Acetate 616 3 Pantothenate 98 7 Alanine 614 2 Pyruvate 587 2 Citrate 452 7 Serine 1185 2 DSS Chemical Shape Indicator 481 9 Taurine 1196 3 Dimethylamine 655 7 Threonine 424 1 Formate 328 3 Trimethylamine 618 8 Fucose 618 2 Urea 332288 8 Bonus compounds There are at least two additional compounds present in trace quantities in this spectrum Identify and profile these compounds and check their concentrations here Suberate 60 6 uM Isopropanol 14 5 uM 10 3 Profiler 115 evomx CHENOMX NMR SUITE USER MANUAL 10 4 Targeted Profiling Targeted profiling involves matching a series of compounds to an experimental spectrum Practically targeted profiling includes the two tasks of identifying a compound or compounds that you would like to profile and matching the individual clusters of each compound to their respective regions of the spectrum Identifying a compound to profile is simply a matter of displaying the compound and visually comparing its signature with visible patterns in the spectrum remembering that you can adjust both height concentration and position frequency during the profiling process There are several methods of filtering and sorting the compound list to include compounds that are most likely to appear in a given region of the spectrum Profiling individual clusters in a region of the spectrum requires some care and attention the most important facet of any profiling technique is
105. ckages developed by Varian Processing layer available in Processor Also the process of choosing coefficients for the parts of a linear combination of real and imaginary spectra derived from the source spectrum and varying linearly with frequency to optimize the appearance of the source spectrum In Profiler a compound with a check in the Pinned column ofthe Compound Table The signatures of pinned compounds always appear in the Spectrum View regardless of what is selected in the Compound Table In Profiler the lines used to indicate pinned compounds Colored to match the default selectionline blue by default or the custom color for each compound if one has been set See portable network graphics Open file format created by Adobe Systems Incorporated Vector graphic format that stores document information in a device independent and resolution independent way Suitable for multiplatform viewing and printing Raster graphic format with lossless compression 48 bit true color depth variable transparency and gamma correction Suitable for image distribution on the internet In Processor an entry that appears in the Processing History to indicate prior processing in third party software packages Appears whenever processed data is imported 1r phasefile ft2 jdf jdx In Profiler the line in the Spectrum View displayed for a compound whose concentration is not set used to estimate the likelihood of the compound b
106. concentration and transforms for the compound as needed see Concentrations on page 52 Transforms on page 53 and Fit Automatically on page 55 If the shape does not appear reasonable continue evaluating the rest of the compounds in the list When you have finished with the filtered list clear the frequency filter to continue your analysis with the full compound list see Quick Searches on page 50 If none of the compounds in the list of potential candidates provides a reasonable shape near the peak that you are investigating consider the possibility that the compound responsible for the peaks is not in your compound library To identify all compounds contributing to a particular region T Select at least one compound set in the Compound Set Panel see Compound Sets Sidebar on page 59 Select a region in the Spectrum View see Select Region on page 22 Filter the Compound Table for compounds in the selected region see Quick Searches on page 50 In the Compound Table select one of the listed compounds Compare the shape ofthe preview line light blue and the spectrum line black and decide whether or not it is reasonable that the preview line could be contributing to the spectrum line in the displayed region If the shape appears reasonable in the region near the peak that you are investigating use the Cluster Navigator to verify that the other clusters for the compound also appear to ma
107. cted compound 6 3 Profiling Tools 47 CHENOMX NMR SUITE USER MANUAL To make more space for the Compound Table you can hide the Spectrum Thumbnail by pressing Ctrl Shift T or clicking View Show Spectrum Thumbnail Related Topics e Change Columns on page 16 e Sidebar on page 16 Preferences on page 25 e Custom Colors on page 48 e Pinned Compounds on page 49 e Starred Compounds on page 50 e Quick Searches on page 50 e Concentrations on page 52 e Maximum Concentrations on page 56 e Compound Set Tools on page 59 e Export Profiled Data on page 60 e Information Tools on page 64 e Concentration Units on page 66 Custom Colors When working with multiple compounds it can become difficult to distinguish which compounds are contributing which parts to an overlapped region You can set specific compounds to appear in colors of your choice whenever they are visible in the Spectrum View How do I set a custom color for a compound 1 Selectthe compound in the Compound Table 2 Clickin the Custom Color column to access the color chooser 3 Clickoneofthe preconfigured colors in the color chooser or click More to choose from a larger selection of colors How do clear a custom color from a compound Compound Selected DE D Compound gt Clear gt Custom 1 Select the compound in the Compound Table Col f e n A 2 Click Clear Custom Color or click in the Custom
108. ctrum Menu Location Icon s File Export Profiled Compounds pack 1 2 6 Open the Export Profiled Compounds dialog Enter a name for the exported compound pack The name you enter is used to label the associated Compound Set when the compound pack is imported into another library via Library Manager Click OK In the resulting file chooser locate the folder in which you would like to save the compound pack In the File Name field type the new name for the compound pack file The specified name can be different from the name of the compound pack itself but you may prefer to keep them the same Click Save Tips and Tricks You and your collaborator each need a valid licensed copy or evaluation edition of Chenomx NMR Suite version 5 0 or later installed to make use of compound packs 6 5 Importing and Exporting Data 61 evomx Menu Location Icon s File gt Import Profile g Menu Location Icon s Tools Spectral Binning CHENOMX NMR SUITE USER MANUAL e Ifyou want to export all of the compounds in a compound set regardless of whether they have been fit in a particular spectrum use Export as Compound Pack in Library Manager Related Topics e Profiling Tools on page 46 e Compound Set Tools on page 59 e Add Compounds on page 97 Export Compounds on page 98 e Compound Set Tools on page 100 Import Profile When you
109. cursor anywhere in the Spectrum View press and hold the Control key Command for Mac OS X and use the mouse scroll wheel to adjust the Horizontal Zoom 4 10 Spectrum View Tools 21 e CHENOMX NMR SUITE USER MANUAL e Press plus or minus to adjust the Vertical Zoom e Press asterisk or slash to adjust the Horizontal Zoom e Middle click anywhere in the Spectrum View to apply an Auto Zoom Spectrum Thumbnail The Spectrum Thumbnail appears in the bottom right corner of modules with a Spectrum View and displays a miniature version of the Spectrum View You can interact with the Spectrum Thumbnail to change the view appearing in the Spectrum View How do toggle the display of the Spectrum Thumbnail Menu Location Vi Show Spectrum 1 Click Show Spectrum Thumbnail umbnail Ctrl Shift T P Hotkey s iln How do I use the Spectrum Thumbnail Cmd Shift T e Click and drag in the Spectrum Thumbnail A red zoom box appears to show you the region you are about to zoom in on and remains to indicate the region currently displayed in the Spectrum View e Click and drag inside the zoom box to move it The Spectrum View updates to show the new region e Click and drag one ofthe solid borders of the zoom box to move that border or click and drag one ofthe corners to move the size and shape of the displayed region e Click anywhere in the Spectrum Thumbnail outside the zoom box to show the entire spectrum in the
110. d currently displayed to select a region Additional information about the selected region appears in the top right corner of the Spectrum View The information displayed always includes the region width in Hz and ppm Depending on the module the display can also include the areas under the compound line overlay line simulation line spectrum line or sum line within the selected region as well as the percentage of the selected area fit by the sum line Profiler only In Profiler you can use the selected region to filter the contents of the Compound Table via Quick Searches Right click on the selected region then click Filter for Compounds in Selected Region The selected region remains in the Spectrum View until you select a new region using the Select Region tool or expand the region to fill the Spectrum View by double or middle clicking inside the region Related Topics Auto Zoom on page 21 Compound Table on page 46 Quick Searches on page 50 4 11 Export Spectrum Image When you prepare publications or presentations based on your work in Chenomx NMR Suite you may need to include images illustrating the fitting process or particular regions of the spectrum You can export spectrum images from any module with a Spectrum View into a variety of bitmap and vector formats How do export an image of the current spectrum Menu Location Icon s File gt Export gt Spectrum Image m 3
111. d in a retrieval system or transmitted in any form or any means electronic or mechanical including photocopying and recording except as permitted in the License Agreement The information contained in this document is subject to change without notice Chenomx Inc assumes no responsibility for any errors omissions or inaccuracies whatsoever Chenomx Inc shall not be held liable for any damages including special or consequential vii evomx CHENOMX NMR SUITE USER MANUAL damages arising out of the use of the information contained in this document and the software described herein even if Chenomx Inc has been advised in advance of the possibility of such damages Chenomx Inc makes no warranties with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose Trademarks Chenomx NMR Suite is a trademark of Chenomx Inc Microsoft Windows Windows XP Windows Vista and Windows 7 are either registered trademarks or trademarks of Microsoft Corporation in the United States and or other countries Mac and Mac OS are trademarks of Apple Computer Inc registered in the U S and other countries Javais a trademark of Sun Microsystems Inc in the United States and other countries Copyright 1992 2010 Sun Microsystems Inc Linux is a registered trademark of Linus Torvalds Other brand and product names are trademarks or registered trademarks of their re
112. d profiles The Sidebar lets you change the lines displayed in the Spectrum View select compound sets to use in fitting spectra and view extended information about the compounds in your Library Legend Sidebar The Legend is an interactive display of the various lines currently appearing in the Spectrum View In Profiler you can use the Legend to pin or unpin compound lines to the spectrum change their colors or make a pinned compound active for fitting How do I pin a compound using the Legend Menu Location File gt Send to Processor Icon s a Ctrl J Hotkey s Cmd J e Menu Location View gt Sidebar gt Legend 1 I a jamms con s a 2 Ctrl Shift L Hotkey s 3 Cmd Shift L Switch to the Legend view in the Sidebar Select a compound in the Compound Table In the Legend view click the gray pin icon appearing to the right ofthe selection line How do I unpin a compound using the pinned lines in the Legend 1 2 3 Switch to the Legend view in the Sidebar Locate a pinned compound in the Legend view Click the red X 3 appearing beside the pinned compound s name How do I unpin a compound using the Legend 1 2 3 Switch to the Legend view in the Sidebar Locate a pinned compound in the Legend view Click the red X 3 appearing to the right of the pinned compound s name 6 6 Information Tools 64 CHENOMX NMR SUITE USER MANUAL How do I unpin a compound using the
113. d quantify user defined compounds using Chenomx NMR Suite You can add the compound signatures that you create with Compound Builder to user defined compound sets using Library Manager and use the resulting sets in Profiler to help you profile spectra You can only use Compound Builder if you have purchased the Professional edition of Chenomx NMR Suite or if you are using the Evaluation edition of Chenomx NMR Suite 8 1 Overview amp Valine pH xcpd Chenomx Compound Builder File Edit View Compound Tools negeemous a E Valine Cluster Center sani rs El 36 23 10 10 Molecular Formula CsH11NO2 Molecular Weight 117 1463 gimol tP IUPAC Name L Valine Alternate CAS Registry Clusters ppm External Database References C ooms Selection e CNN TECLAS S Center ppm 2 26346 PubChem Compound i 3 60363 pe du o Tes CC ee a iL ll 6 20 Peaks 799 81 MHz pH 6 92 Sidebar View Buttons Let you change the currently visible Sidebar view Reference Panel Displays additional information for the compound indicated by the Chenomx Compound ID in the Compound Details including structure molecular weight CAS RN and so on Cluster and Peak Lists Let you edit select or remove clusters or peaks in the currently open compound Also lets you define new clusters based on the currently selected pea
114. d use the Cluster Navigator to view the cluster near 3 5 ppm Adjust the frequency of the pantothenate cluster at 3 51 ppm as needed to match the spectrum Move to the pantothenate cluster near 4 0 ppm and adjust its frequency as needed to match the cluster to the nearest peak in the spectrum The profiled peak for pantothenate in this region does not completely match the area available due to overlap with serine Once you have profiled serine this peak will match better In the Compound Table use Fit Automatically on glycolate and serine and then select serine Use the Cluster Navigator to display the serine cluster near 3 8 ppm and adjust its concentration to better match the spectrum using the sum line to evaluate your progress Use the Cluster Navigator to display the serine clusters at 4 0 and 3 9 ppm Remember that you can click and drag across several clusters to display all of them Adjust the frequencies of the remaining two serine clusters Notice that the sum line over the pantothenate cluster in this region now yields a much better match to the spectrum Select glycolate and adjust the single glycolate peak as needed to match the spectrum 10 3 Profiler 114 evomx CHENOMX NMR SUITE USER MANUAL 27 28 29 30 31 32 Select fucose display the two clusters nearest 3 7 ppm and adjust their frequencies as needed to match the spectrum In the Compound Table select alanine and use F
115. defined including coupled and uncoupled splits Chenomx file format xss designed to store the parameters of simulations created with Spin Simulator Line in the Spectrum View in Spin Simulator corresponding to the overall lineshape of the current spin simulation colored red by default Compound set defined in Library Manager as a set of rules for dynamically selecting compounds from your Library See simplified molecular input line entry specification Data reduction method widely used to prepare spectra for statistical analysis Involves dividing spectra into pieces or bins and considering only the integrated area in each bin for further analysis 151 evomx CHENOMX NMR SUITE USER MANUAL spectral width spectrum details spectrum file spectrum line spectrum overlay spectrum overlay line spectrum thumbnail Spectrum View spin definition Spin Navigator Spin Simulator spin system The full range of frequencies represented in the current spectrum in ppm Information about the currently open spectrum in Processor and Profiler Includes acquisition parameters stored by the spectrometer CSI concentration and spectrum pH determined in Processor and text comments associated with the spectrum Chenomx file format cnx designed to store raw spectrum data fid processing layers added using Processor and profiles created using Profiler You can use spectrum files as overlays in any module w
116. display multiple clusters in the Spectrum View Related Topics Spectrum View Tools on page 20 Compound Table on page 46 Concentrations on page 52 Transforms on page 53 Enforce Transform Windows on page 55 Compound Set Tools on page 59 6 3 Profiling Tools 58 evomx CHENOMX NMR SUITE USER MANUAL 6 4 Compound Set Tools Compound sets are groups containing compounds found in your Library You can use compound sets that you have created in Library Manager to make the task of profiling your spectra easier by placing compounds that interest you the most at your fingertips Compound Sets Sidebar The Compound Sets view lets you modify the contents of the Compound Table to include Menu Location Icon s Hotkey s View Sidebar Compound Sets Ctrl Shift K Cmd Shift K any combination ofthe Compound Sets that you have created in Library Manager The panel contains a list of every compound set that is currently defined Contents of the checked compound sets appear in the Compound Table Tips and Tricks Reference Compound Sets containing any Chenomx Reference Compounds in your library appear automatically in the Compound Sets view Their icons are colored green When you filter the Compound Table by frequency or range only compounds from the currently active compound sets are considered You can use this for example by creating a compound set containing only compounds that appear in urine
117. e 599 48 MHz at pH 7 00 gt E Sum Line f Selection Line e a v Pinned Lines d Glycolate 600 00 Mz L1 Pantothenate F 600 00 MHz Serine 600 00 MHz e Suberate 4 600 00 wk or r A T e Compound Name Concentration uM Maximum uM Sebacate f 27 2 Serotonin 0 0 E Ee oe S Sulfocysteine f 17 4 E ea Suberate 60 6 58 7 l Succinate 18 8 ae pH 7 00 3 9593 ppm 0 457 s Sidebar View Buttons Let you change the currently visible Sidebar view Legend Sidebar view letting you customize the lines appearing in the Spectrum View Cluster Navigator Lets you navigate among the clusters of the currently selected compound You can enable or disable the Cluster Navigator using the View menu Compound Table Displays compounds their calculated concentrations and their fitting status You can access signatures of these compounds in the Spectrum View by selecting them As well you can view additional compound information in the Reference Panel by double clicking on a compound name in this table You can change the default concentration units displayed in the Compound Table using the View menu Spectrum View Tools Let you navigate the spectrum more easily Spectrum View Displays the spectrum as well as the sum line You can modify the display by focusing in on a particular area or displaying and modifying compound signatures Quick Search Lets you filter the Compound Table to focus on a pa
118. e 19 Adda J modifier to SD3 and couple it to SD6 using the larger of the two available uncoupled splits 8 79 Hz Finally you know that this signal should be coupled to SDO and SD1 but the magnitude of the coupling constants is not clear You do have information from some ofthe other couplings in the molecule that suggest the coupling constants should be near 7 Hz so use this as a starting point and fine tune using the J Value Editor Similarly based on the dihedral angles among the protons you can speculate that the coupling constant to SD1 will be larger than the coupling to SDO and bias your adjustments accordingly 20 Add two J modifiers to SD3 one coupled to SDO and the other to SD1 each with a J value of 7 Hz 21 Use the J Value Editor to fine tune the two new J modifiers Ensure that the J value for the coupling to SD1 is larger than the J value for the coupling to SDO Unfortunately there is no entirely satisfactory combination ofthese two coupling constants that results in a good fit of the cluster However the coupling constant to SD2 is still speculative so try adjusting that as well 22 Continue adjusting the J modifiers this time including the coupling to SD2 in your adjustments As before aim for values that center each of the peaks in the spin definition blue on the corresponding peaks in the spectrum black The resulting values are 12 99 Hz to SD2 7 38 Hz to SD1 and 6 65 Hz to SDO 23 Adjustt
119. e available for Chenomx NMR Suite to import Spectra processed from most third party processing software require no additional preparation including XWIN NMR from Bruker Delta from JEOL and NMRPipe Spectra processed elsewhere and converted to JCAMP DX format also require no additional preparation If you have spectra that you processed using VNMR or VNMRJ and you would like to retain the VNMR processing when you import the spectra into Chenomx NMR Suite you will need to copy the phasefile into the fid folder Note that it is possible to automate this process using VNMR if itis something you expect to use often Consult your VNMR documentation for further information on automating tasks To manually copy the Varian phasefile into the fid folder 1 Openthe spectrum in VNMR and process the spectrum 2 Changeexperiments or quit VNMR making note ofthe experiment number in which you have opened the spectrum e g exp2 3 Ina Solaris terminal window copy the datdir folder into the mydata fid folder where mydata fid is your Varian spectrum mydata fidisthe folder that you need to access to open the spectrum using Chenomx NMR Suite Use the following commands cd vnmrsys data mydata fid 2 3 Spectral Data Processing 6 CHENOMX NMR SUITE USER MANUAL cp r vnmrsys expn datdir where expn is the experiment number noted previously and mydata fid is the fid folder you want to access with Chenomx NMR Suite In this examp
120. e in the spectrum see Cluster Navigator on page 58 a Ifthey are present i Profile the non overlapped peaks to help establish a concentration range for the compound see Concentrations on page 52 ii Look for clusters of peaks in the overlapped region with some clearly visible peaks Such clusters occur mostly atthe edges ofthe overlap region but remember to look throughout the region as some peaks stand out nicely between the peaks of another cluster iii Use these partially exposed peaks to establish an optimal frequency for the cluster using transforms see Transforms on page 53 b Iftheyare not present i Look for clusters of peaks in the overlapped region with some clearly visible peaks ii Use these partially exposed peaks to establish an optimal frequency for the cluster using transforms see Transforms on page 53 3 Once you have approximately profiled most of the groups in the overlap region fine tune the heights and frequencies of each cluster in the region to obtain an optimal shape You can use the subtraction line to guide your modifications as a well matched cluster will leave a subtraction line that resembles a normal spectrum with the effects ofthe cluster removed 4 Inoverlap regions profile multi peak clusters before single peak clusters Also if urea is present you may want to profile it last to minimize its interference with other compounds in the spectrum 3 5 Determining Compound
121. e reactivation while minor releases for example version 5 0 to 5 1 do not 1 3 Adding the Chenomx Reference Compounds To add the Chenomx Reference Compounds 1 2 3 4 Open the Library Manager module of Chenomx NMR Suite On the Library menu click Add Compounds Select Chenomx Reference Compounds and click Next Select the frequencies for which you would like to install Chenomx Reference Compounds and click Finish Reference Compound Sets corresponding to the Chenomx Reference Compounds that you added are created automatically 1 3 Adding the Chenomx Reference Compounds 3 Chapter 2 Handling Samples and Spectra Accurate analysis of your NMR spectra with Chenomx NMR Suite requires preparing good samples and acquiring high quality spectra 2 1 Sample Preparation Preparing your samples properly helps you getthe best possible results from your analyses with Chenomx NMR Suite Internal Standard Solution Your samples must contain an internal standard for accurate quantification using Chenomx NMR Suite The internal standard solution recommended for use with Chenomx NMR Suite contains the following components To prepare the Chenomx recommended internal standard solution 1 To the desired volume of 99 996 D 0 add 5 mM 2 2 Dimethyl 2 silapentane 5 sulfonate DSS as a chemical shape indicator CSI and 0 2 w v sodium azide NaN3 to inhibit bacterial growth Remember that DSS is hygroscopic in the solid
122. e spectrum or specific locations in the spectrum Using the Compound Table you can set custom display colors for compounds pin compounds so that they are visible even when you are not working on them and toggle stars on compounds to generally mark them for future reference There are many columns available for display in the Compound Table You can choose to display any number of the available columns with a minimum of one visible at any time and you can drag the column headers to position the columns in any order that you like You can sort the Compound Table on any column by clicking its column header Click the header again to reverse the sort order Tips and Tricks e You must select at least one compound set in the Compound Sets view to see any compounds in the Compound Table e When you have nothing selected in the Compound Table pressing the up or down arrow keys will select the first compound in the Compound Table e After typing in the Quick Search box press the down arrow key to navigate to the first compound in the Compound Table e When you select a compound without a concentration in the Compound Table a preview line for the compound appears in the Spectrum View scaled vertically to suit your current zoom level You can click on the preview line to set the concentration for the selected compound to match the height of the preview line e When you select a compound with a status icon the status area to the left ofthe Q
123. e the spectrum for later analysis in Profiler for creating a simulation in Spin Simulator or for creating a compound signature in Compound Builder 10 2 Processor 109 CHENOMX NMR SUITE USER MANUAL 10 3 Profiler Introduction The Profiler module is the primary tool in Chenomx NMR Suite for profiling sample solutions You can profile samples by matching peak frequencies and heights contained in a compound library with frequencies and heights in the sample spectrum To help you become familiar with the profiling process the first part of the following tutorial provides a step by step guide to fitting a sample spectrum containing only twelve compounds none of which have overlapping signatures The second part provides some techniques for fitting spectra in which some compound signatures overlap Basic Profiling Techniques The simplest way to start analyzing a spectrum is to profile easily identifiable compounds first as they often have additional peaks in the busier regions of the spectrum Profiling them first can help rule out other compounds later in the profiling process In this simple spectrum all of the compounds are quite well separated from each other and should be relatively simple to profile Single Peak Compound Acetate 1 Open Profiler Open the sample file called Samples Profiler Basic Start cnx Zoom in on the single peak near 1 90 ppm Right click on the peak and click Filter for Compounds Near 1 91 ppm w
124. e to review the sample signature for valine do not replace the file called Samples Compound Builder Valine xcpd Complex Compound Proline Now that you have developed a basic familiarity with the tools available in Compound Builder you are ready to use them to build a compound signature for a more complex compound proline 3 6 A Mou N 5 N1 H Creating a Compound Signature for Proline OH 1 Open Compound Builder 2 Importthe proline simulation If you have already completed the Spin Simulator tutorial import the simulation that you created Otherwise import the sample simulation called Samples Spin Simulator Proline xss 3 Select Spectrum cnx and click the Browse button Select the proline spectrum called Samples Compound Builder Proline cnx 4 Open the Compound Details dialog 5 Inthe General tab enter your name as the Compound Author and enter a Sample Concentration of 10 mM 10 6 Compound Builder 131 evomx CHENOMX NMR SUITE USER MANUAL For better integration with compounds based on data from multiple spectrometers including the Chenomx library you may want to replace the specific magnet frequency obtained directly from the spectrum 799 81 MHz with the more general 800 MHz 6 Inthe Reference tab enter the Chenomx Compound ID for proline 230 If you have access to the InChI or SMILES codes for proline you can enter them here as well 7 Inthe Advanced tab enter the m
125. e types select the type that you would like to convert 4 ClickConversion Settings to choose processing options to apply to each spectrum 5 Specify a target folder for the converted spectra Tips and Tricks e Ifthe source folder contains more than one type of spectrum file you need to select one type to convert in the current session since different conversion options may 5 5 Importing and Exporting Data 41 CHENOMX NMR SUITE USER MANUAL apply to each available file type You can do additional sessions to convert other file types e The Conversion Settings available through the Convert Spectra wizard are the same as those available when you import individual spectra Importing Spectra on page 13 e Storing the converted spectra next to the source files means that each new spectrum file appears in the same folder as the spectrum file from which it was created You may find it more useful to have Processor place the converted spectra in a different folder e Ifyou specify a folder other than the source folder for converted spectra you get a folder containing all of the converted spectra with no subfolders created Select Mirror source folder structure to create a folder structure in the target folder that is the same as that in the source folder and store the resulting converted spectra within the new folder structure Related Topics Importing Spectra on page 13 Processing History Sidebar on page 34
126. e your spectrum to retain the changes that you have made to the spectrum pH Related Topics Chapter 2 Handling Samples and Spectra on page 4 Importing Spectra on page 13 CSI Editor on page 31 5 3 Information Tools 33 evomx Menu Location Icon s File gt Spectrum Details CHENOMX NMR SUITE USER MANUAL e Spectrum Details on page 34 Spectrum Details Spectrum details describe the acquisition parameters for the spectrum Your selected CSI and its concentration along with the spectrum pH that you set also appear in the Spectrum Details Since most of these parameters come directly from the imported spectrum you cannot modify most of the spectrum details except for the Frequency Domain Size and Comment fields The Frequency Domain Size field displays the number of points in the Chenomx spectrum cnx in the frequency domain after spectrum data has been imported and zero filling applied You can contrast this with the Time Domain Size which displays the number of point originally present in the imported spectrum in the time domain The Comment field initially consists of the contents of any text descriptor file associated with the original spectrum but you can replace or expand it as desired How do I view and edit details of the current spectrum 1 OpenSpectrum Details 2 Clickanywhere in the Comment field to place a text cursor in the field 3 Make any desired changes 4 Click the
127. echnical Support If you have any questions or concerns please contact Chenomx Technical Support at Phone 1 780 432 0033 Fax 1 780 432 3388 E mail lt support chenomx com gt When you contact Chenomx Technical Support you may be asked to provide an application log The application log contains data that can help us track down issues that you may have experienced while using Chenomx NMR Suite To save an application log file 1 Open the Save Application Log dialog 2 Locate the folder in which you would like to save the application log file 3 Inthe File Name field type a name for the application log file If you do not specify a different name the file is saved as application log 4 Click Save Tips and Tricks e Inthe unlikely event that Chenomx NMR Suite encounters an unrecoverable error and crashes you will be asked to save an application log the next time you run the software We strongly recommend that you do so and send the resulting file to Chenomx Technical Support The information contained in the log file will help us to improve future versions of Chenomx NMR Suite Chenomx is located at 800 10050 112 Street NW Edmonton Alberta T5K 2 1 Canada Disclaimer of Warranties and Liabilities The software described in this document is furnished under a License Agreement The software may be used or copied only in accordance with the terms of such agreement No part ofthis publication may be reproduced store
128. ectral Binning s E Help Menu Q NMR Suite Help F1 F1 td Save Application Log Ctrl Shift A Cmd Shift A s Q Software Activation About Chenomx NMR Suite 6 3 Profiling Tools Profiler provides you with a variety of tools to help you extract compound data from your spectra The data extraction process called profiling includes selecting compounds from your Library setting concentrations determining transforms and finding and using extended information about compounds that you would like to profile Compound Table The Compound Table summarizes the results of your profiling work with the current spectrum It contains entries for compounds that are available to profile in your spectrum as well as those that you have already profiled along with their maximum and profiled concentrations You can modify the display of the Compound Table to show as much or as little information as you like to better suit your preferred approach to profiling 6 3 Profiling Tools 46 evomx CHENOMX NMR SUITE USER MANUAL The currently selected compound in the Compound Table is the active compound in the Spectrum View letting you see its preview line and adjust its concentration and transforms You can filter the current contents of the Compound Table using Quick Searches Filtering can help you quickly find the exact compound that you would like to profile You can filter the table based on text search regions of th
129. ed to a compound by Chenomx staff which uniquely identifies the compound in the Chenomx compound library Compound signatures distributed with Chenomx NMR Suite comprising the complete collection of validated signatures available from Chenomx at all supported frequencies 400 500 600 700 and 800 MHZ Group of peaks that you can move or otherwise adjust as a unit in Compound Builder and Profiler Clusters can correspond to the multiplets familiar to NMR spectroscopists or to arbitrary groupings created in Compound Builder Graphical tool in Compound Builder and Profiler that lets you adjust the Spectrum View to include specific clusters present in the current compound See spectrum file See license file Module in Chenomx NMR Suite that lets you prepare and modify compound signatures xcpd for use in your Library Information about a compound signature created in Compound Builder Some ofthe information appears directly in the reference panel some provides access to other information for display in the reference panel and some indexes the compound within a library Chenomx file format xcpd designed to store the mathematical descriptions of compound signatures created with Compound Builder The compound library of Chenomx NMR Suite consists of a pool of compound files stored in a folder that you can designate via Library Manager preferences 142 evomx CHENOMX NMR SUITE USER MANUAL compound library co
130. eing present in the spectrum Sidebar view showing the processing layers that have been applied to the currently open spectrum Also lets you review the details of each layer and remove layers as needed In Processor one of several modifications that you can make to imported spectrum data to refine the appearance ofthe spectrum and compensate for defects in acquisition Includes phasing baseline correction line broadening reference deconvolution water deletion and reverse spectrum 148 CHENOMX NMR SUITE USER MANUAL ENOMX processing tools Processor profile profiled compounds Profiler proxy server ps pulse sequence Q quick search R Reference Compound Sets In Processor lines and shapes in the Spectrum View illustrating the settings of various processing layers including phasing baseline correction and reference deconvolution Module in Chenomx NMR Suite that lets you import NMR data from various sources add various processing effects like phasing baseline correction line broadening and reference deconvolution and save the results as a spectrum file cnx Part of a spectrum file cnx describing the results of analyzing the spectrum in Profiler Includes the list of identified compounds along with their determined concentrations and transforms Represented in Profiler as the Compound Table In Profiler compounds that have been modified in some way from their original state incl
131. en you click on a spin definition s position the view zooms to provide an optimal view of the spin definition The optimal view includes the full width of the cluster and the full vertical extent of any peaks within the horizontal range You can also use the Spin Navigator to move sequentially through the list of spin definitions in either direction How do I display the spin definitions of a simulation in the Spectrum View 1 Make sure that the Spin Navigator is visible 2 Clicka spin definition s position to zoom directly to that spin definition Click the left or right arrow to move sequentially through the list of spin definitions Tips and Tricks e Click on a spin definition and drag along the Spin Navigator to include adjacent spin definitions in the Spectrum View Related Topics e Spin Systems on page 70 e Spin Definitions on page 71 e Simulation Sidebar on page 75 e Simulation Details on page 76 J Modifiers When you create a new spin definition it appears as a single unsplit peak J modifiers let you split a spin definition into more complex shapes to better fit real spectra J modifiers can be uncoupled affecting only one spin definition or coupled linking the spin definition to another one via its coupling constant Coupled J modifiers result in more accurate simulations as Spin Simulator can use them to calculate higher order coupling effects accounting for tenting and other complex behaviour How do
132. ensity range is visible Increase Decrease Horizontal Zoom Increase Decrease Horizontal Zoom lets you incrementally adjust the horizontal scale of the current view without changing the displayed intensity range Tips and Tricks Decrease Horizontal Zoom is not available when the full frequency range is visible Spectrum View Processor offers a number of useful ways to change the current view by interacting directly with the Spectrum View How do I scroll in the Spectrum View e Use the horizontal and vertical scroll bars appearing at the bottom and right sides of the Spectrum View e Place the mouse cursor anywhere in the Spectrum View then hold down the Shift key and use the scroll wheel on your mouse to scroll horizontally How do I zoom in the Spectrum View e Click and drag directly on the spectrum A red zoom box appears to show you the region you are about to zoom in on e Selecta region using the Select Region tool and double click in the region or right click in the region and select Expand Region The region expands horizontally to fill the Spectrum View e Selecta region using the Select Region tool and middle click in the region or right click in the region and select Auto Zoom Region The region expands horizontally to fill the Spectrum View and an Auto Zoom is applied Place the mouse cursor anywhere in the Spectrum View and use the mouse scroll wheel to adjust the Vertical Zoom e Place the mouse
133. ers that closely matched the spectrum line as determined by comparing the compound and spectrum line shapes near each cluster Estimated upper limit of a compound s concentration calculated automatically by Profiler You can use maximum concentrations to guide analysis of a spectrum in Profiler 146 CHENOMX NMR SUITE USER MANUAL ENOMX N ni NMRPipe NMRPipe processed spectrum data NMRPipe spectrum data no fit normalization normalized intensity O optimize selected peak shapes overlay lines pack pdf peak pH editor See normalized intensity A free software package designed to process NMR spectra Data from spectra processed using the NMRPipe software package Data from spectra stored using the NMRPipe software package Simple profiling technique applied to clusters for which no information is available to guide profiling The cluster is simply not modified In Profiler refers to dividing the area of each bin in a spectral binning session by a common denominator letting you compare binning results across multiple spectra You can normalize bins relative to the total area under the spectrum line or to units of standardized area sa Refers to an intensity relative to that of the tallest peak in the spectrum that is the point with the largest intensity Using this scale if the tallest peak in the spectrum is the creatinine methyl signal and the urea signal is half as tall as the crea
134. ery good approximate shape for the cluster automatically using optimization 13 Moveto the clusters near 1 0 ppm using the Cluster Navigator 14 Select the cluster near 0 98 ppm and click Optimize Selected Peak Shapes 15 Review the optimized shape and refine it as needed To obtain accurate quantification when you use this compound to analyze spectra in Profiler it is helpful to recognize that peak heights have a larger effect on the quantification results than peak width or peak area Thus when you refine the shape of a cluster itis important to ensure that the heights of the peaks match the experimental spectrum particularly well 16 Select the cluster near 1 03 ppm optimize it and refine the shape as needed 17 Move to the cluster near 2 3 ppm using the Cluster Navigator selectit and optimize the shape In this case optimization cannot provide a better solution than the one you started with However when you review the list of peaks in the cluster click on each to view its contribution to the cluster you may notice that there appears to be more peaks present than are strictly necessary Simulation can produce peaks that do not contribute much to the compound at the current frequency Part of building a good compound signature is recognizing these extraneous peaks and removing them 18 Select the first peak in the peak list for the cluster Using the up and down arrow keys flip through the list and observe the contribut
135. es Hotkey s Cmi m 3 Ifnecessary choose a location and filename for the file Tips and Tricks e You cannot close a file that has unsaved changes without having the option of saving the changes If there are no unsaved changes the file is simply closed without further interaction 4 5 Exiting Modules When you are finished working with a module you can exit the module How do I exit a module Menu Location File Exit 1 Click Exit Icon s i 2 Ifyou have made changes to the currently open file and they are not saved choose whether you would like to save the changes 3 fnecessary choose a location and filename for the file Tips and Tricks e You cannot exit a module when a file is open with unsaved changes without having the option of saving the changes If there are no unsaved changes the module exits without any further interaction 4 4 Closing Files 15 CHENOMX NMR SUITE USER MANUAL 4 6 Undo and Redo You can undo recent changes to the currently open file and redo recently undone changes How do I undo a recent change Menu Location Edit gt Undo Redo 1 Click Undo Icon s A y How do I redo a recently undone change Ctrl Z Ctrl Y HOEKEVIS Gnd aromas 1 Click Redo Tips and Tricks e Only the last 100 changes are available to be undone If the change that you want to undo is more than 100 steps back you cannot undo the change e You can only redo changes that you
136. eters and process the resulting data W water deletion Processing layer that masks data points in a spectrum in the frequency domain across a range associated with water Do not confuse water deletion with water subtraction methods that operate in the time domain to remove the water signal itself water suppression NMR technique that reduces the contribution of the water signal to HNMR spectra of aqueous solutions via a special pulse sequences Xcpd See compound file XSS See simulation file XWIN NMR NMR software package developed by Bruker to run their spectrometers and process the resulting data Z zero filling Refers to adding zeros to a fid prior to Fourier transforming it Used by modern spectrometers to ensure that all spectra have a number of points that is a power of 2 enabling the use of fast Fourier transform algorithms Can also increase the digital resolution of a spectrum to a certain extent 155 Index A ACD Labs 5 acquisition time 5 activation key 2 license 2 license file cnxlic 2 multiple users 2 software 2 add Chenomx Reference Compounds 3 97 compound file xcpd 97 compound pack pack 97 J modifier 73 75 old library file cnxlib 97 peak 81 selected compounds to Compound Set 101 spectrum file cnx 97 spin definition 71 spin system 70 ZIP compressed file zip 97 animated zoom 25 annotations custom color 46 48 pin 46 49 star 46 50 applica
137. extrema The resulting lower bound is 0 9581524039197455 when the spectrum pH is 6 92 Bounded Cluster Center and Transform Window The cluster center and transform window operation described above rely on pKas and chemical shifts When the pKas and shifts are determined using observed data and an automatic fitting routine the results of the pKa shift method outside of a certain known pHrange is not reliable as they would require inappropriately extrapolating cluster centers from an arbitrary sigmoidal function The bounded forms ofthese operation are designed to handle such situations The bounded forms are identical to the unbounded forms except for two extra arguments specifying the lower and upper pH boundaries within which the operation is considered valid The value returned by these bounded operations does not change at all outside the valid pH range Results from pHs below the valid lower bound are the same as the result at the lower bound and results from pHs above the valid upper bound are the same as the result atthe upper bound The general form of the bounded cluster center operation is 10 9 Using Expressions 139 evomx CHENOMX NMR SUITE USER MANUAL bClusterCenter lowerBound upperBound ph n pkal pkaN shift1 shiftN 1 where e lowerBound is the lowest pH at which the operation is considered valid e upperBoundis the highest pH at which the operation is considered valid e The remaining arguments a
138. finitions In addition the value itself 11 58 Hz is consistent with the geminal coupling relationship between the protons responsible for these signals 11 Adda J modifier to SD5 and couple it to SD4 using a New Split with a J value of 11 58 Hz The remaining two coupling constants for SD5 are both near 7 Hz the distance from an outermost peak to the adjacent one but it is not clear what the precise values should be You can set them to 7 Hz to approximate the correct value and use the J Value Editors to refine the values visually 12 Add two J modifiers to SD5 as uncoupled splits each with a J value of 7 Hz and a split count of 1 13 Use the J Value Editor to fine tune the J modifiers that you just added Aim for values that center each of the peaks in the spin definition blue on the corresponding peaks in the spectrum black The resulting values are 7 40 Hz and 6 67 Hz 14 Adjustthe frequency height and width of SD5 to better fit the spectrum You can determine the remaining two coupling constants for SD4 using similar techniques The approximate distances are 7 2 Hz 15 Add two J modifiers to SD4 as uncoupled splits with J values of 7 2 Hz each and split counts of 1 16 Usethe J Value Editor to fine tune the J modifiers The resulting values are 7 44 and 6 88 Hz 10 5 Spin Simulator 126 evomx CHENOMX NMR SUITE USER MANUAL 17 Adjust the frequency height and width of SD4 to better fit the spectrum
139. for any more complex baseline fit e When setting breakpoints be aware of the amount of curvature in the area you are trying to fit You need to set more breakpoints to fit regions with very strong curvature such as the areas near the water peak than you would for a relatively flat region Related Topics e Importing Spectra on page 13 Processing History Sidebar on page 34 e Phasing on page 36 e Reference Deconvolution on page 39 e Convert Spectra on page 41 Line Broadening Line broadening is a mathematical operation that multiplies your fid by an exponential function before the fid is Fourier transformed Line broadening effectively increases the linewidth in your spectrum while averaging out instrument noise You may not need to apply line broadening to every spectrum If you choose to use line broadening apply it after phasing and baseline correction While importing a spectrum you may choose to have Processor automatically apply line broadening of 0 to 1000 Hz After importing a spectrum you can apply line broadening manually In either case a Line Broadening layer appears in the Processing History you can remove the layer if necessary How do I apply line broadening to my spectrum Menu Location Processing gt Line Broadening 1 Switch to Line Broadening mode iconos TE 2 Enteravalue between 0 and 1000 Hz Ctrl Alt 3 R Hotkey s 3 Click the Accept button Cmd Alt 3 Tips and Tricks
140. form For accurate concentrations froma Chenomx NMR Suite analysis you must determine the final DSS concentration accurately 2 Foroptional pH measurement in Processor add one or more of 100 mM imidazole 100 mM creatinine and 20 mM DFTMP 3 Adjust the resulting solution to about pH 6 5 Add the internal standard as a 1 in 10 1096 v v spike to each of your samples For example add 70 uL ofthe internal standard to 630 uL of a sample to be analyzed for 700 uL of spiked sample Tips and Tricks e Instead of DSS you may use 3 trimethylsilylpropionate TSP or TMSP or formate as a CSI However we do not recommend TSP or formate as their chemical shifts are sensitive to pH e For accurate sample analysis with Chenomx NMR Suite the pH of your samples should be between 4 and 9 and ideally close to 7 for manual analysis e Spectra that are poorly collected or collected from samples that are poorly prepared may be difficult or even impossible to convert and analyze accurately e Ifyou choose not to add any pH indicators to your samples you need to supply a measured pH value for proper analysis with Chenomx NMR Suite More accurate pH values for your samples allow you to make better use of pH sensitive signatures to profile spectra of the samples 2 1 Sample Preparation 4 CHENOMX NMR SUITE USER MANUAL 2 2 Spectral Data Acquisition For the best results from your analysis with Chenomx NMR Suite you must acquire high quali
141. g Spectra on page 13 Processing History Sidebar on page 34 e Baseline Correction on page 37 e Reference Deconvolution on page 39 e Convert Spectra on page 41 Baseline Correction Baseline correction lets you remove distortions in the baseline of the spectrum You can recognize distorted baselines as a net curvature or slant of the regions of your spectrum that contain no signal noise regions Common forms of baseline distortions include smiles outer regions ofthe spectrum turned up frowns outerregions ofthe spectrum turned down and wings left and right edges of the spectrum turned up or down with the middle region flat If you notice a periodic oscillation or rolling ofthe baseline check the phasing of your spectrum before proceeding with baseline correction Most spectra require some degree of baseline correction particularly if you need accurate quantification in Profiler Apply baseline correction after phasing but before any other processing layers like reference deconvolution While importing a spectrum you may choose to have Processor automatically apply either simple linear baseline correction drift correction or a cubic spline baseline correction based on automatically determined breakpoints After importing a spectrum you can apply automatic or manual baseline correction In either case a Baseline Correction layer appears in the Processing History panel you can remove this layer if necessary
142. ge 90 e Using Expressions on page 135 pH Sensitivities You can make compound signatures that you create in Compound Builder sensitive to the pH ofthe spectrum that you are profiling The clusters of pH sensitive compounds will adapt their centers and transform windows based on the spectrum pH ensuring that they start closer to their actual position in the spectrum and simplifying compound identification in complex regions ofthe spectrum 8 3 Building Tools 88 exomx CHENOMX NMR SUITE USER MANUAL How do I make a compound signature pH sensitive Menu Location Icon s Hotkey s Tools pH Sensitivities Ji w Ctrl Shift P Cmd Shift P 1 No VoB Make sure that you have a set of signatures available to be used as data points on your pH curves They must satisfy the following criteria e All ofthe signatures must have the same number of clusters in the same order e Each signature must have its valid pH set to the pH value from the signature s originating sample via the Compound Details dialog Use a single value instead ofarange Select a signature to use as a master signature This signature will become the pH sensitive signature Open the master signature file xcpd in Compound Builder and overlay the associated spectrum file cnx On the Tools menu click pH Sensitivities Click Load Data Points Click Optimize Lines Review the resulting pH curves for each cluster by cl
143. he frequency height and width of SD3 to better fit the spectrum SD2 has a coupling pattern similar to SD3 You have already coupled it to SD3 and there is only oneremaining J modifier on SD6 to which you can couple Also the coupling constants to SD0 and SD1 should be of similar magnitude to those you just established for SD3 so again start them at 7 Hz Note that the Karplus correlation suggests that this time the coupling constant to SDO should be larger than the coupling to SD1 10 5 Spin Simulator 127 evomx CHENOMX NMR SUITE USER MANUAL 24 Adda J modifier to SD2 and couple it to SD6 using the only remaining uncoupled split 6 52 Hz 25 Add two J modifiers to SD2 one coupled to SDO and the other to SD1 each with a J value of 7 Hz 26 Use the J Value Editor to fine tune the J modifiers Ensure that the J value for the coupling to SDO is larger than the J value for the coupling to SD1 The resulting values are 7 57 Hz to SD0 and 6 87 Hz to SD1 27 Adjustthe frequency height and width of SD2 to better fit the spectrum Since the spin definition overlaps with others on the right hand side use the peaks on the left hand side to guide your adjustments Most of the coupling constants relevant to the last two spin definitions SD0 and SD1 have already been defined There is yet another geminal relationship between the associated protons so couple them using aJ value comparable to the other geminal couplings you ha
144. he new peak appears in the peaks list gets added to the currently selected cluster and becomes the currently selected peak in that cluster How do I add a peak to the current signature Menu Location Icon s Hotkey s Compound Add Peak a Ge Ctrl K Cmd K 1 2 Switch to Add Peak mode The mouse cursor changes to a large crosshair Click somewhere on the spectrum to add a new peak The point that you click defines both the position and the height of the new peak Tips and Tricks To create a new cluster you can deselect all clusters in the cluster list then create a new peak The new peak appears in its own new cluster The new peak appears in the peaklistin numerical order with the currently displayed peaks not necessarily at the beginning or end ofthe list Although the position that you click on the spectrum sets the position and height of the new peak you are free to change both after you have added the peak Right click anywhere in the Spectrum View that does not already contain a peak and select Add a New Peakto Cluster or Add a New Peak to New Cluster to add a new peak to a specific cluster or to a new one respectively When you right click in the Spectrum View to add a new peak the specific cluster to which you can add a peak is the currently selected cluster if only one is selected or the closest cluster to the point that you clicked if multiple clusters are selected 8 3 Building Tools 8
145. he search and restore the full list of compounds Clearing a search also resets the search type to All Tips and Tricks e Use Quick Searches to temporarily limit the number of compounds displayed Use compound sets to define a more permanent working set of compounds for profiling a particular spectrum Related Topics e Compound Table on page 96 e Remove Selected Compounds on page 99 e Compound Set Tools on page 100 Add Compounds You can add compounds to your library from a variety of sources including compound files compound packs Chenomx spectra old Chenomx library files and ZIP compressed archives Add Compounds lets you add compounds from all of these sources to your library making the compound signatures available in Profiler How do add Chenomx Reference Compounds to my library Menu Location Icon s Compounds Add 1 2 3 4 Open the Add Compounds wizard Select Chenomx Reference Compounds then click Next Select the frequencies for which you would like to add Chenomx Reference Compounds Click Finish to add the selected compounds How do add other compounds to my library 1 2 3 Open the Add Compounds wizard Select Importable Files then click the Browse button Select any combination of compound files xcpd compound packs pack spectrum files cnx old Chenomx library files cnx1ib ZIP files zip or folders containing any of the
146. hing protons in the structure of the compound with signals in the spectrum Note that this is often one of the largest tasks in simulating a new compound For proline the assignments are as follows protons labelled a project above the plane ofthe page while those labelled b project below the plane a The signal for proton 4b appears at 1 979 ppm and couples to protons 3a 3b 4a 5a and 5b Spin Definition 0 or SDO The signal for proton 4a appears at 2 012 ppm and couples to protons 3a 3b 4b 5a and 5b Spin Definition 1 or SD1 The signal for proton 3b appears at 2 058 ppm and couples to protons 2 3a 4a and 4b Spin Definition 2 or SD2 The signal for proton 3a appears at 2 339 ppm and couples to protons 2 3b 4a and 4b Spin Definition 3 or SD3 The signal for proton 5a appears at 3 328 ppm and couples to protons 4a 4b and 5b Spin Definition 4 or SD4 The signal for proton 5b appears at 3 413 ppm and couples to protons 4a 4b and 5a Spin Definition 5 or SD5 The signal for proton 2 appears at 4 121 ppm and couples to protons 3a and 3b Spin Definition 6 or SD6 2 Open Spin Simulator 3 Overlay the proline spectrum called Samples Spin Simulator Proline cnx 10 5 Spin Simulator 125 evomx CHENOMX NMR SUITE USER MANUAL 4 Add spin definitions for each of the protons listed in the assignment above making sure that the number of protons for each is set to one Although you do not
147. ialog appears Click Evaluate You can now run Chenomx NMR Suite in Evaluation mode Click the Accept button to run the module that you selected You can view your activation details at any time by clicking Help gt Software Activation in any module Tips and Tricks Ifyou do not have a default e mail client configured or if a message is not automatically generated when you click Request License File you can compose the message yourself To ensure a timely response include your name the version and edition of Chenomx NMR Suite that you would like to activate and the activation key The activation key is unique to the computer used to generate it and you cannot use it to activate the software on other computers If you are installing Chenomx NMR Suite on multiple computers you need to send activation keys for each to Chenomx Chenomx NMR Suite is licensed per seat meaning that one license can be used on one computer Multiple users can use a one seat license To enable multiple users to share a license on the same computer select the license file as described above check the box marked License extends to other users on this computer then click the Accept button Installing a license for all users may require running Chenomx NMR Suite with administrator privileges However once the license is installed all users administrator or not can run Chenomx NMR Suite New major releases for example version 5 x to 6 x requir
148. iately adjacent peaks remove the small peaks 13 more peaks removed c To evaluate the effectiveness of removing a particular peak from the cluster remove it and then select all the peaks contributing to the apparent peak in the spectrum Optimize the subset of peaks and review the results If all ofthe remaining peaks contribute significantly to the optimized shape then move on Otherwise undo the optimization and remove another peak from the subset 15 Review the contributions of each peak in the cluster at 2 011 ppm in the same way as described for the previous cluster 22 peaks removed 16 Select both clusters and optimize them together 17 Refine the shapes of both clusters as needed 10 6 Compound Builder 132 evomx CHENOMX NMR SUITE USER MANUAL Now that the compound matches the spectrum well you can add proper transform windows to each cluster build additional signatures for a pH sensitive compound or make this signature pH sensitive using other signatures as data points 18 Save the compound file If you would like to review the sample signature for proline do not replace the file called Samples Compound Builder Proline xcpd 10 7 Building pH Sensitive Compounds Introduction You can use Compound Builder to build pH sensitive compounds similar to the Chenomx Reference Compounds pH sensitive compounds use expressions incorporating the spectrum pH in place of constant values for certain cluster prope
149. icking the various tabs at the top of the pH Sensitivities dialog Click Accept to apply the automatically generated cluster center and transform window expressions to the clusters in your master signature and set the valid pH of the master signature to the range defined by the pH values of your individual data points Tips and Tricks Clusters that appear green in the Cluster Navigator are pH sensitive meaning that one or more of their heights positions and widths change with spectrum pH If the clusters in your set of signatures appear in different orders in some of the files use Manage Cluster IDs to rearrange the cluster IDs in the signatures so that they match If you manually adjust any cluster after applying pH sensitivities to the compound some or all of the automatically generated expressions may be replaced with constant values If the signatures you use as data points are at a different spectrometer frequency than your master signature you may need to apply an offset to ensure accurate pH curves Click Lock to Current Clusters in the pH Sensitivities dialog to calculate the offset before reviewing and accepting the pH curves If the pH of your master signature is close to a pKa of the compound using Lock to Current Clusters may introduce unintended errors Review the suggested pH curves carefully Related Topics Adjusting Peaks on page 83 Transform Windows on page 86 Manage Cluster IDs on page 90
150. ification results consider verifying the sample concentration that you enter using multiple independent techniques Entering the correct Chenomx Compound ID ensures that information appropriate to the compound appears in the Reference Panel e Ifyouintend to use concentration units of milligrams per decilitre mg dL in Profiler enter a molecular weight e Chenomx calculates molecular weights based on IUPAC atomic weights http www chem qmul ac uk iupac AtWt and rounds the result to four decimal places e You need to save the compound file to retain new or changed Compound Details Related Topics e Reference Panel on page 18 e Building Tools on page 80 e Reference Panel Sidebar on page 91 e Chapter 9 Library Manager on page 94 Information Panel The Information Panel is always visible at the bottom of the Compound Builder window It contains current information about the compound signature as you work on it listing clusters and peaks that you have created describing the elements that you have currently selected and the environment on which your compound is based and letting you access the 8 4 Information Tools 92 CHENOMX NMR SUITE USER MANUAL edit dialog for any clusters or peaks you may have selected You can also select peaks and clusters directly in the Information Panel with more precision than selecting them from the Spectrum View Tips and Tricks e You can select multiple peaks
151. imizes the visible resolution of the data that you collected allowing the most accurate fits possible with your data Clear the Line Broadening check box Unless your CSI linewidths are significantly less than 1 Hz you do not need to add line broadening Clear the Phasing check box For this tutorial we will do manual phasing Since multiple phasing steps are detrimental to spectrum quality turn off the automatic phasing This also disables the option to import phasing angles set in VNMR which should only be retained if you know they are accurate Clear the Auto Baseline Correction check box For this tutorial we will manually correct the baseline Clear the Delete Water Region check box For this tutorial we would like to see what the spectrum looks like before the water region is deleted A warning appears stating that Processor could not determine the pH automatically For this tutorial we will manually measure the spectrum pH Click the OK button Adjusting the Spectrum Phasing 4 Switch to Phasing mode 5 Click the Auto button A good first step to manual phasing is to apply the automatic phasing which often provides a reasonable starting point For the best results visually inspect the automatic results and refine them as needed 10 2 Processor 106 evomx CHENOMX NMR SUITE USER MANUAL 7 Click on Very Fine to make small adjustments to the phasing Drag the sliders for zero order and first o
152. in Chapter 5 Processor e Information Tools on page 64 in Chapter 6 Profiler e Information Tools on page 75 in Chapter 7 Spin Simulator e Information Tools on page 91 in Chapter 8 Compound Builder 4 6 Undo and Redo 16 Enom Menu Location Icon s Hotkey s View Sidebar Legend Ctrl Shift L Cmd Shift L CHENOMX NMR SUITE USER MANUAL Legend The Legend is an interactive display of the various lines currently appearing in the Spectrum View You can use the Legend to toggle the display of each line change their colors or even remove overlays or individual compound lines from the display completely How do toggle the display of a line 1 Switch to the Legend view in the Sidebar 2 Select the check box next to a line to display it or clear the check box to remove it from the Spectrum View How do change a line color using the Legend 1 Click the colored box beside an entry in the Legend 2 Click one of the preconfigured colors in the color chooser or click More to choose from a larger selection of colors How do I remove an overlay using the Legend 1 Clickthe red X beside an overlay entry in the Legend Tips and Tricks e Thetopmost section ofthe Legend Profiler Lines in Profiler Compound Builder Lines in Compound Builder and so on contains the default lines that are always available in the current module Changing the color of a compound line using the Legend in Profi
153. in the spectrum see Identifying Compounds on page 9 Some compounds in the spectrum are very easy to pick out including CSI compounds like DSS or TSP and pH indicators like imidazole creatinine or DFTMP Depending on the type of sample that you are analyzing there may be other compounds that also stand out 6 Systematically review the remaining signals in the spectrum identify and profile as needed You can use information and external links from the Reference Panel see Reference Panel Sidebar on page 65 to help establish the presence of particular compounds in the samples that you are analyzing 3 3 Identifying Compounds Chenomx NMR Suite provides computer assisted methods to profile spectra To identify compounds in a sample you need to match the compound signatures from your library with patterns in the sample spectrum There are several ways that you can identify compounds in a sample The Selection Line must be enabled via the Legend to view individual compound signatures It is enabled by default To identify specific compounds 1 Select at least one compound set in the Compound Sets view see Compound Sets Sidebar on page 59 2 Locate a compound in the Compound Table that you believe is present in the sample and select it see Compound Table on page 46 3 For each cluster compare the shape of the preview line light blue and the spectrum line black and decide whether it is reasonab
154. in this panel e f you have just accidentally removed a layer in the Processing History you can use the Undo button to restore it Related Topics e Chapter 2 Handling Samples and Spectra on page 4 Importing Spectra on page 13 Legend on page 17 e Processing Tools on page 35 e Convert Spectra on page 41 5 4 Processing Tools Processor applies each processing step as alayer altering the way that you see and interact with your spectrum but leaving the original raw data untouched The Processing History records each layer along with its associated parameters like phase angles baseline breakpoints and linewidth adjustments You can review the layers and even remove them if necessary restoring your spectrum to earlier state s When you import a processed spectrum processing that you have performed in other software appear in the Processing History as a layer called Preprocessing the details of the Preprocessing layer indicate the format from which the processed data was imported The Preprocessing layer is not reversible and cannot be removed If you need to work with the 5 4 Processing Tools 35 evomx CHENOMX NMR SUITE USER MANUAL spectrum as it appeared before processing in other software import the raw data fid jdf fid directly Phasing Phase correction or phasing lets you correct phase shifts that may have occurred during data acquisition You can recognize phase shifts in a spectrum as
155. ing 62 subtraction line fit 118 sum line fit 119 supported file types Bruker processed data 1r 13 CHENOMX NMR SUITE USER MANUAL Bruker spectrum file fid 13 JCAMP DX spectrum file jdx 13 JEOL Delta spectrum file jdf 13 NMRPipe processed data ft2 13 NMRPipe spectrum file fid 13 Varian processed data phasefile 6 13 Varian spectrum file fid 13 T tape measure see selected region target linewidth 39 temperature 5 time domain size 34 total area 31 62 transform window clear 86 88 default 86 edit 86 enforce 53 55 transposed layout see export TSP see CSI tutorial compounds proline 125 131 134 valine 122 129 134 U uncoupled split 73 undo zoom 20 ungroup selected splits 73 UUID 91 V valine 122 129 134 Varian processed data phasefile 6 13 spectrum file fid 13 vertical zoom 21 VNMR 5 VNMRj 5 Ww water deletion 40 suppression 120 wings 37 X X scale 24 XWIN NMR 5 Y Y scale 24 Z zero order phase 36 zoom animated 25 auto 21 box 21 22 horizontal 21 initial 25 redo 20 set 20 show entire spectrum 20 undo 20 vertical 21 159
156. ing and specify a target folder for the resulting binned data You can specify a series of spectrum files or one or more folders containing spectrum files as the source If you would like to repeat a binning session that you have previously saved you can specify a binning configuration file BinningConfiguration xml to import 6 5 Importing and Exporting Data 62 evomx CHENOMX NMR SUITE USER MANUAL Choose a binning method to apply to the specified spectra You can use a defined bin size in ppm across a range of the spectrum in ppm or a defined number of bins You can also use bins based on the transform windows of compounds in a selected Compound Set targeted binning If you would like to reuse a predefined set of bins you can specify a bin definition file BinDefinitions txt to load Choose regions ofthe spectrum to exclude from binning if desired You can specify any regions ofthe spectrum using start and end values in ppm Choose a binning target You can bin spectra based on the sum line standard binning or the subtraction line residual binning Choose a normalization method You can normalize the bins relative to the total area under the spectrum line or to units of standardized area sa where 1 sais the area under a theoretical DSS methyl peak at 0 50 mM Tips and Tricks Binning can take a long time especially on older computers or particularly large datasets If you have never tried binning before try a
157. ing Peaks on page 83 e Transform Windows on page 86 e Cluster Navigator on page 90 e Information Panel on page 92 Optimize Selected Peak Shapes Adding peaks to a signature and adjusting them to approximately model a particular region ofthe spectrum is fairly simple However the task of fine tuning those peaks to accurately match the lineshape in that region can be tedious Once you have approximated the shape of a region of the spectrum you can use Compound Builder s optimization algorithms to rapidly obtain a more refined match to that region How do I optimize the shape of peaks in my compound signature 1 Selectthe peaks and clusters that you would like to optimize 2 Click Optimize Selected Peak Shapes Tips and Tricks e You must select fewer than 100 peaks to optimize Optimization will generally give better results if your starting shape is reasonably close to the actual shape ofthe spectrum Simulating the compound in Spin Simulator can often give you a very good starting shape Related Topics e Add Peak on page 81 e Selecting Peaks and Clusters on page 82 e Adjusting Peaks on page 83 e Generate Cluster for Region on page 86 8 3 Building Tools 85 evomx Menu Location Icon s Hotkey s Tools Generate Cluster for Region P il Ctri Shift I Cmd Shift I CHENOMX NMR SUITE USER MANUAL Generate Cluster for Region You may need to build a compound signature tha
158. ing formate as a CSI finding the CSI automatically does not work If the automatic method does not work you need to define the CSI manually If you would like to adjust the height or width of the CSI peak while keeping its total area constant check the Preserve CSI Area box Define CSI parameters in the CSI Editor only after you have finished applying all necessary processing layers In particular if you change the line broadening or add 5 3 Information Tools 31 CHENOMX NMR SUITE USER MANUAL reference deconvolution you need to set new CSI parameters to ensure accurate quantification and generally good fits e Finding the DSS or TSP peak automatically relies on having the water peak centered in the spectrum The formate peak cannot be located automatically Related Topics e Chapter 2 Handling Samples and Spectra on page 4 Importing Spectra on page 13 e pH Editor on page 32 e Spectrum Details on page 34 e Processing Tools on page 35 pH Editor Signal position and shape for compounds in aqueous solution can be very sensitive to pH The accuracy of the pH that you set for a spectrum may have an impact on the quality and accuracy of fits that you may perform in Profiler Compound Builder or Spin Simulator based on the spectrum The pH editor lets you calculate or set the pH for the current spectrum If your sample contains any combination of creatinine imidazole or DFTMP Processor may be able to calculate the
159. ing the simulation frequency and numbers of spin systems transitions and J modifiers represented in the simulation currently selected spin definitions e O00 O Spin Navigator Lets you navigate among the spin definitions of the currently open simulation You can enable or disable the Spin Navigator using the View menu Spectrum View Tools Let you navigate the spectrum more easily Spectrum View Displays the spectrum overlay as well as the simulation line and the Spectrum Thumbnail Displays a thumbnail image of the current spectrum You can also use the thumbnail to navigate the Spectrum View at various zoom settings Status Bar Displays the current cursor position in the units specified by the View gt X Scale and View gt Y Scale settings Also displays information about recent user actions 7 2 Quick Reference Guide Linux Windows Mac OS X File Menu P New Simulation Ctrl N Cmd N Open Ctrl O Cmd O g Open Recent sad Close Ctrl W Cmd W H Save Ctrl S Cmd S n Save As s Ly Export gt Spectrum Image Preferences Exit _ Edit Menu V Undo Ctrl Z Cmd Z W Redo Ctrl Y Cmd Y m Copy Spectrum Image to Clipboard Select All Ctrl A Cmd A View Menu X Scale eee Y Scale ees lol Zoom Show Entire Spectrum Ctrl Minus Cmd Minus 7 2 Quick Reference Guide 68 CHENOMX NMR SUITE USER MANUAL Enom Li
160. ion View gt Edit Mode gt CSI 1 Menu Location Tools gt Find CSI Automatically 2 mp Icon s gt 3 4 5 Switch to the CSI Editor Select the CSI present in your sample using the Chemical Shape Indicator drop down box Valid CSIs for use in Chenomx NMR Suite include DSS TSP and formate Type the concentration of the CSI in your sample in the Concentration mM text entry box Automatic Click the Find Automatically button Manual e Click and drag the CSI peak to match it with the spectrum line black e Adjust the width by dragging the width control red triangles to either side of the peak or typing a number directly into the Width Hz text entry box e Use the up and down arrow keys to adjust peak height and the left and right arrow keys to adjust peak position Tips and Tricks If Processor cannot find the CSI automatically when you use DSS or TSP check the phasing and baseline correction of your spectrum and try again If Processor still cannot find your CSI you need to use the manual tools to locate it instead To adjustthe CSI settings for your spectrum Processor must be in the CSI Edit Mode Processor cannot automatically find formate as a CSI due to potential overlap with other compounds If you have selected DSS as the CSI then the indicated center position always reads 0 ppm If you use TSP or formate instead the center position varies based on the current pH value for the spectrum If you are us
161. ions scaling concentrations and clearing concentrations transforms custom colors pins or stars Stars are saved in the spectrum file and remain visible when you next open the file or until you clear them How do star a compound 1 Click the grey star for the compound in the Starred column of the Compound Table How do I clear a starred compound 1 Selectthe compound in the Compound Table 2 Inthe Compound menu click Selected Compound Clear Star or click the yellow star for the compound in the Starred column Tips and Tricks e Starring a compound adds it to the Profiled Compounds set even if you have not set concentrations or transforms for the compound e Stars are stored with the spectrum when you save it as a cnx file The compound that you star remains starred when you next open the file until you clear the stars e You can export the starred status of all compounds to a file using Export Profiled Data Related Topics e Compound Table on page 46 e Custom Colors on page 48 e Pinned Compounds on page 49 e Concentrations on page 52 e Transforms on page 53 e Maximum Concentrations on page 56 e Scale Concentrations on page 57 Quick Searches When you are profiling a spectrum you may have several compound sets active The number of compounds appearing in the Compound Table can make it difficult to locate a particular compound to profile Quick Searches let you tempor
162. ions of each peak The first two peaks 2 234 and 2 240 ppm appear normal but the next two peaks both very near 2 243 ppm appear almost identical but offset slightly Near identical pairs of peaks are excellent candidates for pruning as the two peaks could be replaced with one without any significant change in the overall shape 10 6 Compound Builder 130 Enom CHENOMX NMR SUITE USER MANUAL 19 Find all of the near identical pairs of peaks in the cluster and remove one peak from each pair 6 peaks removed Further review reveals that some of the taller peaks in the spectrum are represented by groups of three peaks one tall central peak flanked by two much shorter peaks The flanking peaks can also be removed without reducing the shape quality 20 Find all ofthe groups of three peaks as described above and remove the two flanking peaks from each group 6 groups 12 peaks removed 21 Optimize the shape of the cluster again The results of the second optimization are much better and require only minimal refinement In addition you have now reduced the complexity of the model from 38 peaks to 20 while improving the overall quality of the fit Now that the compound matches the spectrum well you can add proper transform windows to each cluster build additional signatures for a pH sensitive compound or make this signature pH sensitive using other signatures as data points 22 Save the compound file If you would lik
163. ire Spectrum Ctrl Minus Cmd Minus Zoom Undo Zoom Zoom Redo Zoom 8 2 Quick Reference Guide 78 exomx CHENOMX NMR SUITE USER MANUAL Linux Windows Mac OS X Zoom gt Set Zoom Ctrl M Cmd M I Zoom Select Region Ctrl T Cmd T y Zoom Auto Zoom Ctrl F Cmd F Te Zoom gt Increase Vertical Zoom Zoom gt Decrease Vertical Zoom Zoom Increase Horizontal Zoom 7 e Zoom Decrease Horizontal Zoom Sidebar Legend Ctrl Shift L Cmd Shift L amp Sidebar gt Reference Panel Ctrl Shift R Cmd Shift R Show Sidebar Ctrl Shift S Cmd Shift S Show Spectrum Thumbnail Ctrl Shift T Cmd Shift T Show Cluster Navigator Ctrl Shift N Cmd Shift N Compound Menu Add Peak Ctrl K Cmd K n Edit Selected Peaks Ctrl E Cmd E x Delete Selected Peaks Delete Delete L Group Selected Peaks as Cluster Ctrl G Cmd G be Transform Window gt Edit for Selected Ctrl Shift E Cmd Shift E Cluster Transform Window gt Set Default on u un Selected Clusters Transform Window Clear for Selected Clusters 4 Transform Window gt Set Default on All u Qlusters ba Transform Window gt Clear for All Clusters lt Previous Cluster Q Q gt Next Cluster E E Tools Menu uF Set Spectrum Overlay Ctrl Shift O Cmd Shift O m Clear Spectrum Overlay 8 2 Quick Reference Guide CHENOMX NMR SUITE USER MANUAL evomx
164. it Automatically Display the alanine cluster near 1 5 ppm and adjust it as needed to match the spectrum Use the right most peak to set the height for the cluster much like you did for the basic spectrum Return to the alanine cluster near 3 8 ppm and adjust its frequency as needed to match the spectrum using the sum line to evaluate your progress Adjust the frequencies of each of the fucose clusters near 3 8 ppm Try finding individual peaks in each cluster that match peaks in the spectrum and lining them up Adjust the frequencies of each of the remaining fucose clusters as needed If there is not enough ofa pattern visible in the spectrum to which you can match a cluster leave the cluster in its original position 33 In the Compound Table select urea and and use Fit Automatically 34 Adjust the urea cluster near 5 8 ppm as needed to match the spectrum 35 Check the overall shape of the spectrum to verify that the sum line lies generally along the spectrum line You can check your results for all of the compounds with the following list of concentrations If you are unsure what the finished profile should look like open the file Advanced End cnx to view this spectrum with profiling completed Table 10 2 Expected Concentrations for Advanced Start cnx Compound Conc uM Compound Conc uM 2 Oxoglutarate 620 9 Fumarate 155 5 3 Indoxylsulfate 448 7 Glycolate 852 1 4 Hydroxy 3 methoxymandelate 50 2 Nia
165. ith a Spectrum View Line in the Spectrum View in Processor and Profiler corresponding to the experimental data of the currently open spectrum colored black by default Spectrum files cnx appearing in the Spectrum View as supplements to the currently open file In Spin Simulator and Compound Builder overlays guide you in constructing accurate simulations and compound signatures In Processor and Profiler they let you compare the currently open spectrum with others in the same dataset or other datasets Line in the Spectrum View in Compound Builder and Spin Simulator corresponding to the spectrum overlay colored black by default Miniature version ofthe Spectrum View that you can use to quickly navigate or zoom to different regions of the spectrum regardless ofthe currently viewed region or zoom level Main display area in Processor Profiler Compound Builder and Spin Simulator Contains the spectrum graph and several tools for manipulating the displayed information including the Cluster Navigator or Spin Navigator and controls for adjusting the heights and frequencies of displayed peaks clusters or spin definitions Basic element of a simulation created in Spin Simulator Each spin definition consists of a number of protons a center in ppm and a width in sw Adjusts the Spectrum View in Spin Simulator to include specific spin definitions in the current simulation Analogous to the Cluster Navigator Module in Chenomx NM
166. its entry and selecting Send to Compound Builder As soon as you save your changes in Compound Builder they are available in all Compound Sets containing the compound e You can also double click a compound in the Compound Table to send it to Compound Builder Related Topics e Change Columns on page 16 e Quick Searches on page 96 e Send to Compound Builder on page 99 e Remove Selected Compounds on page 99 e Compound Set Tools on page 100 Quick Searches The number of compounds appearing in the Compound Table can make it difficult to locate a particular compound Quick Searches let you temporarily limit the number of compounds appearing in the Compound Table based on search criteria The search criteria can include text searches based on name compound IDs comments or all of these 9 3 Library Tools 96 evomx CHENOMX NMR SUITE USER MANUAL How do limit the compounds visible in the Compound Table Icon s Hotkey s T Click the binoculars icon at the left edge of the search box to choose the type of search to use Compound Name Compound Comment Chenomx Compound ID or All If you do not select something here the default search type is All Type your search terms in the Quick Search box at the top left ofthe Compound Table The contents ofthe Compound Table updates to show all compounds matching your current entry Click the clear button at the right edge of the search box to cancel t
167. ively move as you adjust the pH You can determine a coarse pH simply by adjusting these lines as close as possible to the corresponding peaks in your spectrum 33 Using the coarse pH and the information box to the left of the pH slider bar note which pH indicator is most active in the pH range of the spectrum In this case it is imidazole If the coarse pH is near the transition between creatinine and imidazole around 5 5 then both indicators are useful in refining the pH value 34 Zoom in onthe two peaks for imidazole Click the Automatic Vertical Zoom button to ensure the best view of the two peaks The range of pH available on the slider bar changes as you zoom in to yield a finer grained control over your pH adjustments To make the entire range of 0 14 available clear the Fine Tune check box 35 Click and drag the pH slider bar to adjust the pH or manually enter a pH value in the pH text entry box As before the indicator lines move as you adjust the pH To obtain a refined pH value ensure that each line is as close as possible to its associated peak keeping in mind that every change in pH can move both peaks Once again the measured pH should be around 8 37 36 Click the Show Entire Spectrum button to restore a view of the whole spectrum Once you have finished adjusting your spectrum in Processor you can e Movethe spectrum directly to Profiler for further analysis using the Jump to Profiler button e Sav
168. ks Compound sets that you change in Library Manager update immediately in Profiler Profiler does not close when you open Library Manager Also you can leave Library Manager open for future reference while you continue your work in Profiler 6 4 Compound Set Tools 59 CHENOMX NMR SUITE USER MANUAL Related Topics Compound Set Tools on page 59 Chapter 9 Library Manager on page 94 6 5 Importing and Exporting Data You can export data from your profiled spectra for further analysis bin the spectra for analysis by more traditional techniques or create images ofthe spectra for use in publications and presentations Export Profiled Data When you have finished profiling a spectrum or set of spectra you often need the resulting data in a spreadsheet or statistical analysis package Export Profiled Data lets you create a text file containing all of the relevant details from profiled spectra in a format that you can easily open in software like Microsoft Excel or Umetrics SIMCA P How do I export data from one or more spectra Menu Location Icon s File Export Profiled Data txt 83 1 2 Start the Export Profiled Data wizard Choose the source spectra to export and specify a target folder and filename for the exported text file You can specify the currently open spectrum other individual spectrum files or one or more folders containing spectrum files as the source Selectthe type of data th
169. ks or clusters Cluster Navigator Lets you navigate among the clusters of the currently open Spectrum View Tools Let you navigate the spectrum more easily cluster s or peak s 00 6 and peak s compound You can enable or disable the Cluster Navigator using the View menu Spectrum View Displays the spectrum as well as the sum line and the currently selected Information Panel Displays information relating to the currently selected cluster s 8 1 Overview 77 Enom CHENOMX NMR SUITE USER MANUAL Spectrum Thumbnail Displays a thumbnail image of the Spectrum View The thumbnail can also be used to navigate the spectrum at various zoom settings Status Bar Displays the current cursor position in the units specified by the View gt X Scale and View gt Y Scale settings Also displays information about recent user actions 8 2 Quick Reference Guide Linux Windows MacOS X File Menu P New Compound Ctrl N Cmd N Open Ctrl O Cmd O Open Recent Close Ctrl W Cmd W L3 Save Ctrl S Cmd S Save As PES g Import Simulation us Ly Export gt Spectrum Image A Compound Details ak Preferences E Exit 2 Edit Menu Undo Ctrl Z Cmd Z Redo Ctrl Y Cmd Y m Copy Spectrum Image to Clipboard Select All Ctrl A Cmd A Select by Cluster Ctrl B Cmd B View Menu X Scale es Y Scale es xs lel Zoom Show Ent
170. le In Compound Builder itis the compound matching the Chenomx Compound ID that you have specified in the Compound Details Tips and Tricks e Some sections in the Reference Panel are collapsed by default including Alternate Names and Alternate CAS Registry To expand them click the symbol next to the section name Click the symbol to collapse the section again e Each ofthe External Database References are links to the indicated database Click a linkto open the associated database entry for the current compound in your system s web browser e Chenomx NMR Suite retrieves all Reference Panel information from a Chenomx server named reference chenomx com to ensure that you always have the most accurate information If you access the internet through an HTTP proxy server or have no internet access you may want to change the internet preferences for Chenomx NMR Suite e f Chenomx NMR Suite cannot access the internet the content of the Reference Panel will instead come from a local cached copy Related Topics Preferences on page 25 e Profiling Tools on page 46 e Building Tools on page 80 e Compound Details on page 91 Processing History The Processing History view in Processor tracks processing effects that you add to a spectrum recording details about each effect and letting you reverse them as needed Related Topics Processing History Sidebar on page 34 Compound Sets The Compound Sets view in Profi
171. le expn would be exp2 2 3 Spectral Data Processing 7 Chapter 3 Common Tasks Chenomx NMR Suite can help you to perform many useful tasks You can find overviews of some common tasks in this chapter Detailed descriptions of each function mentioned here appear in later chapters 3 1 Processing a Spectrum Before you analyze a spectrum in Chenomx NMR Suite whether in Profiler or in Compound Builder you need to process the spectrum To process a spectrum in Processor 1 u e w N Open the spectrum see Opening Files on page 13 and Importing Spectra on page 13 If necessary reverse the spectrum plot Reverse Spectrum flips the spectrum in the frequency domain Reversing is only necessary for some Bruker spectra Adjust the phasing see Phasing on page 36 Apply baseline correction see Baseline Correction on page 37 as needed Define the CSI parameters see CSI Editor on page 31 Optional Apply reference deconvolution to correct lineshape distortions see Reference Deconvolution on page 39 or apply line broadening to improve the signal to noise ratio see Line Broadening on page 38 If you applied reference deconvolution or line broadening readjust the CSI parameters to take into account any newly introduced changes in lineshape see CSI Editor on page 31 Determine the sample pH using imidazole creatinine or DFTMP see pH Editor on page 32 Option
172. le importing a spectrum you may choose to have Processor apply water deletion automatically After importing a spectrum you can apply water deletion manually In either case a Water Deletion layer appears in the Processing History panel you can remove this layer if necessary Tips and Tricks e Water deletion will not work if you have not defined the CSI for the spectrum as the location of the water peak is determined relative to your CSI e f your spectrum needs to be reversed but is not yet reversed water deletion may not work as intended If necessary reverse the spectrum before applying water deletion Related Topics Importing Spectra on page 13 e CSI Editor on page 31 Processing History Sidebar on page 34 e Reverse Spectrum on page 41 e Convert Spectra on page 41 5 4 Processing Tools 40 CHENOMX NMR SUITE USER MANUAL Reverse Spectrum Reverse spectrum reverses the order of the data points in your spectrum in the frequency Processing Advanced gt Reverse domain effectively flipping the spectrum horizontally Menu Location Spectrum You only need to use reverse spectrum with certain types of spectra from Bruker leone as spectrometers If you have trouble locating the CSI peak when you have a CSI in the sample Ctrl Alt G or even making any sense of your spectrum after importing it you may need to reverse the PU Cmd Alt 6 spectrum While importing a spectrum you may choose
173. le that the preview line could be contributing to the spectrum line in the displayed region 4 Ifthe shape appears reasonable click the preview line and adjust the resulting shape by determining appropriate heights and transforms for the clusters of the compound see Concentrations on page 52 and Transforms on page 53 5 Ifthe shape does not appear reasonable continue by selecting another compound in the Compound Table To identify possible compounds causing a specific peak 1 Selectatleastone compound set in the Compound Sets view see Compound Sets Sidebar on page 59 2 Right click on the peak and click Filter for Compounds Near x xx ppm 3 3 Identifying Compounds 9 evomx CHENOMX NMR SUITE USER MANUAL In the Compound Table select one of the listed compounds to display the preview line and Cluster Navigator for the compound see Cluster Navigator on page 58 Compare the shape of the preview line light blue and the spectrum line black and decide whether or not it is reasonable that the preview line could be contributing to the spectrum line in the displayed region If the shape appears reasonable in the region near the cluster that you are investigating use the Cluster Navigator to verify that the other clusters for the compound also appear to match reasonably well see Cluster Navigator on page 58 If all clusters appear reasonably well matched apply an automatic fit then adjust the
174. lea Eee Pyrimidine 800 00 3 99 to 8 63 04 May 2009 2008 Chenomx Inc Pyroglutamate 800 00 4 19 to 9 23 04 May 2009 2004 Chenomx Inc By chrenom 700 mz Pyruvate 800 00 4 05 to 8 93 O4 May 2008 2004 Chenomx Inc Quinolnate 800 00 4 20 10 8 81 24 Apr 2009 2004 Chenomx Inc Riboflavin 800 00 4 42 108 79 03 Apr 2008 2004 Chenomx Inc D Tutorial Compounds Ribose 800 00 4 12 to 8 97 30 Apr 2009 2004 Chenomx Inc Saccharopine 800 00 4 08 to 8 96 24 Mar 2009 2008 Chenomx Inc S Adenosylhomocysteine 800 00 4 04 to 9 05 24 Apr 2009 2005 Chenomx Inc i Salicylate 800 00 4 07 to 8 97 17 Apr 2009 2004 Chenomx Inc Salicylurate 800 00 4 12 to 8 76 19 May 2009 2004 Chenomx Inc Sarcosine 800 00 4 09 to 8 84 17 Apr 2009 2004 Chenomx Inc Sebacate 800 00 4 39 to 9 08 24 Apr 2009 I 2008 Chenomx Inc 4 09 to 8 96 96 2004 Chenomx Inc Serotonin 800 00 3 97 to 9 05 04 May 2009 2008 Chenomx Inc sn Glycero 3 phosphocholine 800 00 3 94 to 9 06 25 Mar 2009 2008 Chenomx Inc S Sulfocysteine 800 00 6 00 to 8 00 05 May 2009 2004 Chenomx Inc S berate 800 00 4 00 to 8 88 24 Apr 2009 2004 Chenomx Inc 4 k 800 00 4 00 to 8 92 04 May 2009 2004 ChenomxInc Succinylacetone 800 00 4 14 to 8 68 22 Apr 2009 2004 Chenomx Inc Sucrose 800 00 4 27 to
175. legacy compound album cca to guide building a new compound signature How do I import a spin simulation or compound album Menu Location File Import Simulation 1 Open the Import Compound dialog g eee d 2 Locate the folder containing the simulation or album file that you would like to import 8 3 Building Tools 80 Enom CHENOMX NMR SUITE USER MANUAL 5 Select the simulation or album file and click Open Choose a calibration method If you are calibrating to a spectrum file cnx click the Browse button and locate the spectrum file you would like to use The spectrum that you choose is overlaid in the Spectrum View Click OK Tips and Tricks Calibrating to the Default Environment instead of a spectrum file will set a magnet frequency of 800 MHz a pH of 7 00 and CSI settings corresponding to DSS at 0 500 mM height of 1 si width of 1 sw The magnet frequency and spectrum pH for the current spectrum overlay appear in the status bar at the bottom of the Compound Builder window If there is no spectrum overlay the displayed values correspond to the default environment You must calibrate a signature to a real spectrum for accurate results when using the signature in an analysis Related Topics Spectrum Overlays on page 19 Chapter 7 Spin Simulator on page 67 Compound Details on page 91 Add Peak Add Peak lets you add a new peak to the current compound signature T
176. ler is equivalent to setting a custom color using the Compound Table The custom color is saved with the spectrum and will be used when the spectrum is reopened All other color changes made via the Legend are temporary and are reset to default colors the next time you run Chenomx NMR Suite e You can change the default colors of various lines in a module using the preferences for that module e Each of the default lines for a module can be toggled on or off temporarily using the Legend To change the default state of these lines use the Preferences for the module that you would like to change Related Topics e Spectrum Overlays on page 19 Preferences on page 25 e Compound Table on page 46 e Custom Colors on page 48 4 8 Sidebar 17 evomx Menu Location Icon s Hotkey s View Sidebar Reference Panel wy Ctrl Shift R Cmd Shift R CHENOMX NMR SUITE USER MANUAL Reference Panel The Reference Panel Sidebar view displays information about specific compounds The displayed information includes a structure image molecular formula and weight alternate names and links to external reference sites You can use this information to verify the identity ofthe compound that you are fitting and better understand the signature and behaviour of the compound in your spectra The compound represented in the Reference Panel in Profiler is the compound that you currently have selected in the Compound Tab
177. ler lets you modify the contents of the Compound Table to include any combination of the compound sets that you have created in Library Manager The panel contains a list of every compound set that is currently defined Contents of the checked compound sets appear in the Compound Table Related Topics e Compound Sets Sidebar on page 59 4 8 Sidebar 18 e CHENOMX NMR SUITE USER MANUAL Simulation The Simulation view lets you select view and edit elements ofthe currently open spin simulation including spin systems spin definitions and J modifiers Related Topics e Simulation Sidebar on page 75 4 9 Spectrum Overlays You can overlay Chenomx spectra cnx in any module with a Spectrum View Overlaying aspectrum in Compound Builder or Spin Simulator can aid the fitting process while overlays in Profiler and Processor can provide useful visual references to other spectra in a dataset How do I overlay spectra MM Tools Add Spectrum Overlays 1 ClickAdd Spectrum Overlays Set Spectrum Overlay in Spin Simulator and Tools Set Spectrum Overlay Compound Builder tudo m 2 Locate the folder containing the spectra that you would like to overlay and select Ctrl Shift O the spectra Hotkey s s daEm 5hiTt 3 Click Overlay How do I remove a single spectrum overlay 1 Inthe Legend view of the Sidebar click the red X beside the overlay that you would like to remove How do I remove all spectr
178. leucine and the triplet near 0 92 ppm lets you confirm the identification It is reasonable that isoleucine is present at or near 9 uM E010 Isoleucine 9 um z Cluster 5 Po diuster 4 Cluster 3 Cluster 2 0 08 0 03 0 10 0 08 0 06 0 06 pos pot 0 04 Feo V 001 N J M uh Ww aa uM A Vw emis caes AP PM Y WS i m A 1 gt r A e 0 A lt gt A 4 365 3 60 2 00 1 95 1 50 1 45 1 30 15 1 20 Figure 10 11 There is no clear information elsewhere in the spectrum to guide the placement of the remaining clusters so they are left at their default positions The initial assessment of isoleucine at 9 uM is still consistent with the spectrum 10 5 Spin Simulator Introduction You can use Spin Simulator to create spin simulations of compounds that you would like to add to your library Simulations that you create in Spin Simulator can be imported into Compound Builder to create compound signatures that you can then add to your library You may find itis helpful to have the molecular structure ofthe compound you are simulating available for reference purposes You can only complete the Spin Simulator tutorial if you have purchased the Professional edition of Chenomx NMR Suite or if you are using the Evaluation edition of Chenomx NMR Suite Simple Simulation Valine To become familiar with the various tools avail
179. lusters by selecting them via the Spectrum View or the Information Panel e Right click on a selection in the Spectrum View or Information Panel and select Delete Peaks to delete the selected peaks Related Topics e Add Peak on page 81 e Selecting Peaks and Clusters on page 82 e Information Panel on page 92 Adjusting Peaks In most cases the initial location of a peak does not accurately match the spectrum overlay You need to modify the height or frequency of one or more peaks to arrive at a signature that satisfies your requirements How do I set peak properties to specific values Menu Location Compound gt Fall Selected 1 Select the peaks or clusters that you would like to adjust Wane ay 2 Open the Edit Selected Peaks dialog Ctrl E 3 Enterthe desired center position in ppm amplitude height in si and width in Hotkeys Cmd E sw to apply to all selected peaks or clusters 4 Click OK How do adjust peak properties 1 Select the peaks or clusters that you would like to adjust 8 3 Building Tools 83 evomx CHENOMX NMR SUITE USER MANUAL Do any of the following e Click and drag the selected peaks or clusters in the Spectrum View to adjust their positions and heights Use the blue triangles on the horizontal and vertical axes for fine control over position and height respectively e Click and drag the blue triangles on either side of the selected peaks and clusters at approxim
180. m check the spectrum pH and consider increasing the pH uncertainty value If while Enforce Transform Windows is on you try to move a cluster that has been set outside its transform window the cluster will first snap to its nearest transform window edge After that you can move it normally within its transform window Related Topics pH Editor on page 32 Compound Table on page 46 Transforms on page 53 Cluster Navigator on page 58 Transform Windows on page 86 Maximum Concentrations The maximum concentration of a compound in Profiler is an estimate of the upper limit of the compound s concentration Profiler calculates this value as the maximum concentration for the compound that does not result in any peak in the compound s signature exceeding the height of the spectrum line or any cluster moving outside its tranform window The value is made available as a guideline only How do I set a compound to its maximum concentration Menu Location Icon s Compound Selected Compound Set to Maximum Concentration vj 1 Select the compound in the Compound Table If you do not see the compound in the Compound Table select additional compound sets or use Quick Searches to find it On the Compound menu click Selected Compound gt Set to Maximum Concentration or right click on the compound and select Set to Maximum Concentration from the context menu 6 3 Profiling Tools 56
181. m data and applying zero filling In Profiler a quick search based on the position of peaks in the spectrum in ppm You can specify a single frequency or a range of frequencies resulting in a list of all compounds having at least 144 evomx CHENOMX NMR SUITE USER MANUAL ft2 generate cluster for region gif graphics interchange format grouping J modifiers group peaks as cluster imidazole InChl IUPAC international chemical identifier Java runtime environment JCAMP DX spectrum data jdf jdx one transform window that overlaps the specified frequency or range A more limited variety of a text filter See NMRPipe processed spectrum data In Compound Builder an operation that automatically creates a series of peaks to match the selected region by minimizing the average intensity of the subtraction line See graphics interchange format Raster graphic format with lossless compression 8 bit palette color depth and simple transparency support Suitable for image distribution on the internet In Spin Simulator combines multiple uncoupled J modifiers into asingle one with the same total split count and the average J value for the group For example grouping three uncoupled splits with split counts of 1 2 and 3 and J values of 4 6 and 7 Hz will give a single uncoupled split with a split count of 6 1 243 and a J value of 5 67 Hz average of 4 6 and 7 Hz In Compound Builder defi
182. maries 60 transposed layout 60 exported data txt 31 expressions 83 86 F file operations close 15 open 13 save 14 filter compounds 50 compounds in selected region 50 compounds near x xx ppm 50 find CSI automatically 31 find pH automatically 32 first order phase 36 CHENOMX NMR SUITE USER MANUAL fit automatically 55 folder default 25 formate see CSI frequency domain size 34 frowns 37 G generate cluster for region 86 graphics interchange format gif 23 group peaks as cluster 84 selected splits 73 H horizontal zoom 21 identify compound based on a peak 9 based on a region 9 image file types encapsulated PostScript eps 23 graphics interchange format gif 23 portable document format pdf 23 portable network graphic png 23 scalable vector graphic svg 23 imidazole 4 8 32 import compound album file cca 80 profile 62 simulation file xss 80 spectrum 13 information panel 82 83 initial zoom 25 installation 1 Linux 1 Mac OS X 1 Windows 1 internal standard 4 J J coupling 75 J modifier add 73 75 coupled split 73 delete 73 75 edit 73 75 group selected 73 J value 73 J value editor 73 list 73 split count 73 uncoupled split 73 ungroup selected 73 J value 73 J value editor 73 Java 1 JCAMP DX spectrum file jdx 13 JEOL Delta spectrum file jdf 13 JRE see Java K keyboard shortcut cluster adjustmen
183. md T y Zoom Auto Zoom Ctrl F Cmd F Te Zoom gt Increase Vertical Zoom Zoom gt Decrease Vertical Zoom e Zoom Increase Horizontal Zoom m e Zoom Decrease Horizontal Zoom Sidebar gt Legend Ctrl Shift L Cmd Shift L amp Sidebar gt Reference Panel Ctrl Shift R Cmd Shift R D Sidebar gt Compound Sets Ctrl Shift K Cmd Shift K Show Sidebar Ctrl Shift S Cmd Shift S Show Spectrum Thumbnail Ctrl Shift T Cmd Shift T Show Cluster Navigator Ctrl Shift N Cmd Shift N EM Change Columns Compound Menu Selected Compound Submenu EH Clear Concentration xs mn ba Clear gt Transforms x Q Clear Custom Color ent amp Clear gt Pin amp Clear gt Star sx x Clear gt Everything Delete Delete 8 Fit Automatically Space Space NE Set to Maximum Concentration lt Previous Cluster Q Q 6 2 Quick Reference Guide 45 Enom CHENOMX NMR SUITE USER MANUAL Linux Windows Mac OS X gt Next Cluster E E Starred Compounds and All Compounds Submenus E Clear Concentrations ane ba Clear gt Transforms Q Clear Custom Colors ane 4 Clear Pins m E Clear Stars z5 x Clear gt Everything NJ Set to Maximum Concentrations Eg Scale Concentrations m Tools Menu ud Add Spectrum Overlays Ctrl Shift O Cmd Shift O ur Remove All Spectrum Overlays S f Filter Compounds Sp
184. me way Many spectra can benefit from the use of reference deconvolution but it is not required It is particularly useful in reducing the effects of varying shimming techniques or when you need accurate quantification from regions with strong overlap of signals You need to apply reference deconvolution manually after you have imported your spectrum After you have applied reference deconvolution a Reference Deconvolution layer appears in the Processing History panel you can remove this layer if necessary How do apply reference deconvolution to my spectrum 1 Inthe CSI editor fit the red CSI peak to your spectrum See CSI Editor on page 31 for details 2 Switch to Reference Deconvolution mode 3 Zoominto the highlighted peak in the Spectrum View 4 Ifyou are using DSS or TSP as a CSI select the Use DSS TSP Satellites check box Otherwise clear the check box 5 Enter the desired target linewidth 6 Clickthe Accept button to apply your changes or click the Cancel button to discard them 7 In CSI Edit mode refit the red CSI peak to your spectrum to account for changes introduced by reference deconvolution See CSI Editor on page 31 for details Tips and Tricks e Only apply reference deconvolution after you are satisfied with the phasing and baseline correction in your spectrum e Thetargetlinewidth text box initially contains the native linewidth of your spectrum based on your CSI definition e Choosing a
185. mpound Table select additional compound sets or use Quick Searches to find one 2 Click and drag the blue triangle on the vertical axis of the graph upward until the compound signature reaches the desired height If the compound s concentration is already set you can click and drag any peak or cluster vertically to change the concentration How do I clear a concentration 1 Selecta compound with a concentration in the Compound Table If you do not see any compounds with concentrations in the Compound Table make sure that you have selected the Profiled Compounds set If you still do not see any compounds with concentrations then the current spectrum has no concentrations set 2 Inthe Compound menu click Selected Compound Clear Concentration or right click on the compound in the Spectrum View or the Compound Table and click Clear Concentration The compound s concentration in the Compound Table appears as unknown Tips and Tricks You can have Profiler suggest concentration and transform values for the currently selected compound by clicking Compound gt Selected Compound gt Fit Automatically or by pressing the space bar e You can double click on a compound s concentration in the Compound Table and type a value directly to set the concentration Type a number from 0 to 5000 mM or equivalent concentrations in uM or mg dL or type to set the concentration to unknown e When you have selected a compound in the
186. mpound line compound line fit compound pack compound set Compound Sets view Compound Table coupled split creatinine CSI CSI editor CSI line default transform window A pool of compound files xcpd stored in a common folder and indexed by Library Manager used to profile spectra in Profiler In Compound Builder the line in the Spectrum View indicating the overall shape ofthe compound signature colored red by default Simple profiling technique involving matching the currently selected compound line blue to the spectrum line black Chenomx file format pack designed to store a collection of compound files xcpd for exchange among users of Chenomx NMR Suite List of compounds defined in Library Manager that appears in Profiler for use during profiling Can refer to any set appearing in the Compound Sets view or to fixed lists of compounds specifically as opposed to the automatically updating lists known as smart compound sets Sidebar view appearing in Profiler and Library Manager that contains a list of available compound sets based on the current compound library Lets you modify the displayed contents of the Compound Table to aid in profiling spectra Table appearing in Profiler and Library Manager Contains information on compounds in your Library including names compound IDs valid magnet frequencies and pH ranges InChI and SMILES strings and so on Also contains maximum and measured
187. mpounds animated zooming application log auto baseline correction auto phasing auto zoom baseline correction best guess fit See Bruker processed spectrum data Refers to the period of active data collection in an NMR pulse sequence The recommended acquisition time for spectra intended for use with Chenomx NMR Suite is 4 s The process of licensing Chenomx NMR Suite for legitimate use involving the installation of a Chenomx license file cnxlic Refers to expanding the compound library by adding signatures from one or more compound sources including the Chenomx Reference Compounds compound packs pack compound files xcpd and legacy Chenomx NMR Suite files cnx and cnxlib Smooth transitions between zoom settings in the Spectrum View of Processor Profiler Compound Builder or Spin Simulator Text file that Chenomx NMR Suite generates for troubleshooting purposes Option available on importing spectra into Processor or Profiler to automatically determine placement of breakpoints for spline based baseline correction Equivalent to selecting Auto Spline during baseline correction in Processor Option available on importing spectra into Processor or Profiler to automatically determine phase angles Equivalent to selecting Auto during phasing in Processor Adjusts the vertical scale of the Spectrum View in Processor Profiler Compound Builder and Spin Simulator to include all visible data from availa
188. nd create and edit compound sets using the compounds in your library Sources of compounds that you can add to your library include the Chenomx Reference Compounds compound files xcpd created in Compound Builder compound packs pack from Chenomx or from other users of Chenomx NMR Suite embedded libraries in legacy spectrum files cnx and legacy Chenomx library files cnx1ib Adding Compounds To use compound signatures that you create using Compound Builder you need to add them to your library Adding compound files xcpd makes the compounds available in your library letting you use them in Profiler add them to compound sets and generally use them alongside the Chenomx library Adding Valine and Proline to Your Library 1 2 3 Open Library Manager Click Library Add Compounds Select Importable Files then click the Browse button and navigate to the folder in which you saved the compound files that you created during the Compound Builder tutorial If you have not completed the Compound Builder tutorial you can use the provided sample files in the Samples Compound Builder folder Select your compound files and click Choose Files If you are using the sample files select Valine pH xcpd and Proline xcpd and click Choose Files Click Next 10 8 Library Manager 134 evomx CHENOMX NMR SUITE USER MANUAL 6 Click the Create associated compound set check box and enter a name for the new
189. nd signatures you can access extended information about common compounds view and update details associated with the current compound and more precisely manage peaks and clusters in complex compounds Reference Panel Sidebar The Reference Panel Sidebar view displays information specific to the compound matching xam View Sidebar Reference the Chenomx Compound ID that you have specified in the Compound Details The displayed enu Location Panel information includes a structure image molecular formula and weight alternate names itonts e and links to external reference sites You can use this information to better understand the structure and behaviour of the compound as you build its signature Ctrl Shift R Honeys emdshiftk Related Topics e Reference Panel on page 18 e Preferences on page 25 e Building Tools on page 80 e Compound Details on page 91 Compound Details Using Compound Details you can associate information with compound signatures that Menu Location File Compound Details you build The information that you enter lets you usethe signature with appropriate spectra 3 display correct information in the Reference Panel calculate accurate concentrations and Gud E manage the contents of your compound library effectively Table 8 1 Compound Details General Compound Name Name ofthe compound as you would like it to appear in the Compound Table in Profiler Compound
190. ndows and the associated valid pH range For the best results when you add the compound to your library you also need to add some descriptive metadata about the compound OH Creating a Compound Signature for Valine 1 Open Compound Builder 2 Importthe valine simulation If you have already completed the Spin Simulator tutorial import the simulation that you created Otherwise import the sample simulation called Samples Spin Simulator Valine xss 3 When prompted to calibrate the simulation environment select Spectrum cnx and click the Browse button Select the valine spectrum called Samples Compound Builder Valine cnx The compound signature that you build will become part of your compound library To ensure that the new compound is properly represented in your library you need to add some basic information about the compound itself Some information has been filled in automatically based on the calibration spectrum that you selected 4 Open the Compound Details dialog 5 Inthe General tab enter your name as the Compound Author and enter a Sample Concentration of 10 mM For better integration with compounds based on data from multiple spectrometers including the Chenomx library you may want to replace the specific magnet frequency obtained directly from the spectrum 799 81 MHz with the more general 800 MHz 6 Inthe Reference tab enter the Chenomx Compound ID for valine 215 If you have access to the
191. near water around 4 73 ppm its signal may be obscured by the presence ofthe water peak Baseline correction or solvent suppression during processing may further affect quantification Use obscured clusters only when no alternative is available and recognize that concentrations based solely on obscured clusters may be unreliable Table 10 1 Expected Concentrations for Basic Start cnx Compound Conc uM Compound Conc uM 3 Indoxylsulfate 458 2 Formate 321 2 4 Hydroxy 3 methoxymandelate 49 1 Fumarate 155 6 Acetate 613 8 Niacinamide 564 4 Alanine 608 3 Pantothenate 94 7 Citrate 432 1 Pyruvate 598 9 DSS Chemical Shape Indicator 481 9 Urea 147094 0 Advanced Profiling Techniques Real samples are rarely as simple as the previous example and usually contain compounds whose signatures overlap Although profiling becomes more challenging in these cases the strategy remains the same profile easily identifiable compounds first and use the contributions of those compounds to refine your efforts at profiling the overlapped regions There is a certain artistry to efficiently profiling a complex spectrum The best method for learning many of the techniques that you can use to profile such a spectrum is practice profiling progressively more complex spectra until you develop a level of proficiency More detailed discussions of profiling strategies are available elsewhere in this manual see Targeted Profiling on page 116
192. nes a collection of peaks as belonging to the same cluster so that they will transform together appear under the same entry in the Cluster Navigator and obey the same transform windows pH indicator supported by Chenomx NMR Suite Most accurate for pH 5 50 to 8 80 See IUPAC international chemical identifier A string of characters that uniquely represents a chemical compound based on its structure Developed and approved by the International Union of Pure and Applied Chemists IUPAC and the National Institute of Standards and Technology NIST Software based on a specification by Sun Microsystems that lets a computer run Java applications like Chenomx NMR Suite Spectrum data unprocessed or processed stored in the JCAMP DX data interchange format See JEOL Delta spectrum data See JCAMP DX spectrum data 145 evomx CHENOMX NMR SUITE USER MANUAL JEOL Delta spectrum data J modifier J value J value editor Legend library Library Manager license file line broadening M magnetic equivalent matched clusters maximum concentration Data from spectra acquired using JEOL spectrometers and processed where applicable using the Delta software package developed by JEOL In Spin Simulator a parameter modifying a spin definition by splitting it to form more complex shapes Composed of a J value and a split count and includes both coupled and uncoupled splits In Spin Simulator defines
193. ngle DSS peak at the far right side of the spectrum Use the Automatic Vertical Zoom button to ensure the best view of the single peak Accurately fitting the CSI peak helps you getthe most accurate quantification possible from your spectra Click the Find Automatically button to have Processor attempt to match the peak automatically If your spectrum has poor phasing or baseline correction finding the CSI automatically will not work readjust the phasing and baseline correction before proceeding When you process spectra using formate as a CSI the automatic fit will not work you will need to use the manual fit instead If necessary use the Adjustment Handle width controls or keyboard controls to adjustthe shape ofthe red overlaid peakto match the black spectrum line as closely as possible Many ofthe CSI parameters interact to affect the quality of the analysis that is possible with your spectra Perhaps most obviously the CSI peak position calibrates the chemical shift scale In addition the CSI concentration and peak height both 10 2 Processor 107 evomx CHENOMX NMR SUITE USER MANUAL 18 affect quantification accuracy while and accurate CSI peak width allows you to better fit regions of the spectrum in which multiple clusters overlap While you are zoomed in to the CSI peak apply reference deconvolution Reference deconvolution corrects your spectrum for some types of systematic errors that may have occurred d
194. ns that you would like to link and select the uncoupled split that will link it to the other spin definition 2 Open the Edit Selected J Modifier dialog 3 Select Coupled and select the spin definition to which you would like to link 4 Selectthe uncoupled split from the second spin definition that you would like to link to 5 Click OK How do delete a J modifier 1 Selecta spin definition 2 Selecta J modifier that you would like to delete 3 Click Delete Selected J Modifier How do uncouple a J modifier 1 Selecta spin definition 2 Select a J modifier that you would like to uncouple 3 Click Uncouple How do ungroup J modifiers 1 Selecta spin definition 2 Select an uncoupled split with a split count greater than 1 3 Click Ungroup Selected Splits How do group several J modifiers 1 Selecta spin definition 2 Select several uncoupled splits that you would like to combine Hold down Ctrl to multi select J modifiers 3 Click Group Selected Splits Tips and Tricks e J Modifiers can only link two spin definitions that are in the same spin system 7 3 Simulating Tools 74 CHENOMX NMR SUITE USER MANUAL e When you delete a coupled J modifier you will delete it from both spin definitions to which it applies If you only want to delete the J modifier from one spin definition uncouple it first e Uncoupling a coupled J modifier will result in an uncoupled split on each of the two
195. nt to the infix operation sqrt arg1 Returns the square root of the sqrt 25 5 supplied value Trigonometric Operations acos arg1 For a value representing an acos 1 3 141592653589793 m angle in radians returns its arc atos 1 0 cosine in the range 0 through rt pi asin arg1 For a value representing an asin 1 1 5707963267948966 1 2 angle in radians returns its arc asin 0 0 sine in the range 1 2 through 7 71 2 atan arg1 For a value representing an atan 1 0 7853981633974483 1 4 angle in radians returns its arc tanto 0 tangent in the range 1 2 atan through 1 2 cos arg1 For a value representing an cos 1 angle i ee TENTHS its cos 3 14159 0 9999999999964793 1 cosine sin arg1 For a value representing an sin 0 angleinradians returnsitssine iot 14150 2 65358979335273E 6 0 ofthe value tan arg1 For a value representing an tan 0 angle in radians returns its tangent of the value tan 785398 0 9999996732051568 1 10 9 Using Expressions 137 CHENOMX NMR SUITE USER MANUAL Chemistry Related Expressions In addition to the basic operations described above Chenomx NMR Suite supports a number of chemistry related expressions allowing a sort of shorthand notation for certain commonly encountered situations Cluster Center The cluster center operation computes the center chemical shift of a cluster based on a given pH value and a sigmoid function with pote
196. ntain any number of protons and spin definitions as long as the total number of transitions is less than 2000 If you need to create a simulation requiring more than 2000 transitions you will need to use multiple spin systems The total number of transitions in the current simulation appears in the simulation details see Simulation Details on page 76 Heightadjustments always affect the whole simulation not just the currently selected spin definition If you need to adjust the heights more than is possible in Spin Simulator save the simulation and open it in Compound Builder then make your adjustments there Deleting a spin definition also deletes any J modifiers that you have associated with that spin definition Related Topics Spin Systems on page 70 Spin Navigator on page 73 J Modifiers on page 73 Simulation Sidebar on page 75 7 3 Simulating Tools 72 evomx Menu Location View gt Show Spin Navigator Ctrl Shift N Hotkey s steh md Shift 5 Compound Add New Menu iA J Modifier Icon s ay Ctrl J Hotkey s Cmd J CHENOMX NMR SUITE USER MANUAL e Simulation Details on page 76 Spin Navigator The Spin Navigator lets you quickly move among the spin definitions that you have created in the current simulation It appears in the top left corner ofthe Spectrum View as a ordered list of the approximate positions of all the spin definitions of the simulation in ppm Wh
197. ntially more than one set of inflection points and plateaus For the purposes of this operation inflection points or pka values are interpreted as acid dissociation constants for the compound being modeled and the sigmoid plateaus describe the ppm locations chemical shifts of each pure species associated with the dissolved compound The general form of the cluster center operation is clusterCenter ph n pkal pkaN shift1 shiftN 1 where e phisthe pH ofthe solution the compound is dissolved in represented by the spectrum pH for the currently overlaid spectrum e nis the number of pka values for the modeled compound must be at least 1 e pkal pkaNarethe compound s pka values dissociation constants in ascending order there must be exactly n ofthese These values are in the same units as pH e shift1 shiftN 1 are the pure species chemical shifts associated with the given pka values and the cluster being modelled They are in the same order as the their associated pkas Note that there must be exactly n 1 of these These values are expressed in ppm The following expression is an example of a valid use of the cluster center operation clusterCenter ph 3 0 6902281 6 851296 9 289176 4 3607736 0 9786361 0 9779636 0 9253154 The above example describes a cluster from a compound with 3 pKas of about 0 69 6 85 and 9 29 and plateaus at about 4 361 0 979 0 978 and 0 925 ppm The resulting cluster
198. nu Location Icon s Hotkey s View Zoom Show Entire SEHE Show Entire Spectrum lets you quickly expand the current view setting both the vertical lel and horizontal scales to their largest possible values Ctrl Minus Tips and Tricks Cmd Minus e Show Entire Spectrum is not available when the full spectrum is already visible e Show Entire Spectrum is applied by default when you first open any spectrum unless you have set specific zoom settings in the Preferences Related Topics e Preferences on page 25 Set Zoom Menu Location View gt Zoom gt Set Zoom You can set the Spectrum View to display specific frequency horizontal and height vertical ronis E ranges Displaying specific ranges can be useful for preparing illustrations or focusing on a Ctrl M particular area of the spectrum Hotkey s Cmd M How do I zoom to specific frequency and height ranges 1 Open the Set Zoom dialog 2 Enter the horizontal range X Axis in ppm that you would like to display or select Entire Axis to zoom out to the full spectrum width 3 Enter the vertical range Y Axis in standard intensity si that you would like to display or select Entire Axis to zoom out to the full spectrum height 4 ClickOK Tips and Tricks e When you open the Set Zoom dialog the values that appear initially correspond to your current view If you change the values in only one dimension your current settings in the other dimension
199. nux Windows Mac OS X w Zoom gt Undo Zoom R Zoom gt Redo Zoom Zoom Set Zoom Ctrl M Cmd M I Zoom Select Region Ctrl T Cmd T y Zoom Auto Zoom Ctrl F Cmd F Te Zoom gt Increase Vertical Zoom Zoom gt Decrease Vertical Zoom e Zoom Increase Horizontal Zoom T e Zoom Decrease Horizontal Zoom Sidebar Legend Ctrl Shift L Cmd Shift L Sidebar Simulation Ctrl Shift D Cmd Shift D Show Sidebar Ctrl Shift S Cmd Shift S Show Spectrum Thumbnail Ctrl Shift T Cmd Shift T Show Spin Navigator Ctrl Shift N Cmd Shift N Show J Value Editor Ctrl Shift J Cmd Shift J Simulation Menu Add New Spin System C Delete Current Spin System Oj Add New Spin Definition Ctrl D Cmd D x Delete Current Spin Definition nes J Add New J Modifier Ctrl J Cmd J Jj Edit Selected J Modifier Jg Delete Selected J Modifiers e Uncouple Selected Split E sss 3 Group Ungroup Selected Splits lt Previous Spin Definition Q Q gt Next Spin Definition E E Tools Menu 7 2 Quick Reference Guide 69 Enom Menu Location Icon s Hotkey s File New Simulation d Ctrl N Cmd N CHENOMX NMR SUITE USER MANUAL Linux Windows Mac OS X ud Set Spectrum Overlay Ctrl Shift O Cmd Shift O m Clear Spectrum Overlay NMR Suite Help NMR Suite Help F1 F1 Ld Save Application Log Ctrl Shift A Cmd
200. of such concentrations depends on the accuracy ofthe molecular weight provided To change the molecular weight associated with a compound open it in Compound Builder and edit the Compound Details Related Topics e Profiling Tools on page 46 e Open Library Manager on page 59 e Export Profiled Data on page 60 e Compound Details on page 91 e Send to Compound Builder on page 99 6 6 Information Tools 66 Chapter 7 Spin Simulator Spin Simulator is a simple yet powerful tool for creating simulations of NMR spectra based on user defined spin systems and reference spectra You can use these simulations as starting points for creating your own compound signatures especially if you need to create signatures at multiple magnet frequencies or you want to create robust signatures with a strong theoretical backing To use Spin Simulator effectively you must have a basic understanding of NMR theory and know howto interpret NMR spectra especially J coupling Simulating complex compounds requires at least this basic theoretical knowledge Chenomx experts can provide compound fitting services and develop specialized compound libraries for you For more information about customizing compound libraries and related services please contact Chenomx Contract Services You can only use Spin Simulator if you have purchased the Professional edition of Chenomx NMR Suite or if you are using the Evaluation edition of Chenomx NMR Suite
201. ofthe signatures in your library 3 Reference Deconvolution if necessary You will not need to apply reference deconvolution to every spectrum but when you do make sure that you have properly adjusted the phasing and baseline correction first 4 Line Broadening 0 to 1000 Hz if necessary Line broadening is available but many 1H NMR spectra will not need it If you have CSI linewidths of 1 to 1 5 Hz or higher do not apply line broadening 5 Water Deletion Variation in the performance of solvent suppression pulse sequences can produce water peaks that are still much larger than all the other signals in the spectrum When you do not expect any signals of interest very close to the water peak 10 1 File Location Note 105 CHENOMX NMR SUITE USER MANUAL 4 68 4 88 ppm deleting the water peak can greatly reduce the amount of zooming in you will need to do while profiling the spectrum Processing a Spectrum Getting Started 1 Open Processor 2 Open the spectrum Sample fid fid 3 Inthe Import Varian Raw FID Dialog a Select DSS as the Chemical Shape Indicator and set its concentration to 0 484 mM Setting an accurate CSI concentration ensures that quantification in Profiler is as accurate as possible When you import your own spectra use a CSI concentration appropriate to your samples Expand the Advanced Details section Set Zero Fill to to Automatic if it is not set already Zero filling max
202. olecular weight of proline to four decimal places 115 1305 Also enter a valid pH of 6 93 Enter noesy as the pulse sequence 8 ClickOK 9 Setdefault transform windows on all clusters and make sure that the subtraction line green is visible Several clusters are quite easy to adjust and do not overlap with any other clusters so refine these ones first 10 Optimize each ofthe clusters near 4 1 3 4 3 3 and 2 3 ppm respectively and refine them as needed The cluster near 2 1 ppm overlaps slightly with the cluster near 2 0 ppm but the overlap should not cause any particular difficulty However the cluster does include some extraneous peaks so remove them before proceeding 11 Moveto the cluster near 2 1 ppm select it and optimize the shape 12 Review the contributions of each of the peaks to the overall cluster shape Delete peaks that appear particularly small relative to the peaks immediately adjacent 6 peaks removed 13 Optimize the cluster and refine it as needed The remaining two clusters are heavily overlapped and optimizing them at this point yields unsatisfactory results You will need to simplify both of these clusters before refining their shapes 14 Review the contributions of each peak in the cluster at 1 979 ppm to the overall shape ofthe cluster a For pairs of near identical peaks remove one peak from each pair 8 peaks removed b Forgroups containing peaks much smaller than the immed
203. ompound set 103 reverse spectrum 41 rolling 37 S sample concentration 91 sample preparation 4 scalable vector graphic svg 23 scale concentrations 57 select cluster 82 peak 82 region 22 selected region 22 send to Compound Builder 99 Processor 64 Profiler 42 set to maximum concentration 56 zoom 20 show entire spectrum 20 sidebar 16 24 Compound Builder 91 compound sets 18 59 100 legend 17 64 processing history 18 34 Profiler 64 reference panel 18 65 91 simulation 19 75 Simulator 75 simulation details 76 file xss 13 70 80 frequency 76 158 Enom new 70 sidebar 19 75 spin definition 71 spin system 70 71 smart compound set 100 102 103 smiles 37 spectral binning bin definitions 62 bin label 62 bin size 62 bin width 62 binning configuration file 62 binning target 62 exclude region 62 normalization 62 output options 62 total area 62 spectral width 5 spectrum Bruker fid 13 file cnx 13 41 JCAMP DX jdx 13 JEOL Delta jdf 13 NMREPipe fid 13 overlay 19 pH 32 remove overlays 19 reverse 41 thumbnail 22 Varian fid 13 spectrum image copy to clipboard 24 export 23 spectrum thumbnail 22 24 Spectrum View 21 58 73 spin definition add 71 delete 71 edit 71 navigator 73 panel 70 spin system add 70 delete 70 split count 73 star 46 50 statistical analysis export profiled data 60 spectral binn
204. on in the text box for a transform window indicates that you may use an expression to set the transform window e When you create pH sensitive compounds expressions for the transform windows are calculated automatically based on the set of spectra that you select e Atransform window applies to the center ofa cluster not the positions of its outermost peaks Consider only cluster centers when you manually set transform windows for your compounds e When you manually set a transform window for a cluster the cluster center must lie within the selected limits e After you have set a transform window for a cluster if you try to move the cluster beyond either limit of the transform window the limit moves to accommodate the new position of the cluster If the transform window was an expression adjusting it in this manner will replace the expression with a constant You may need to acquire multiple spectra to determine appropriate transform windows for a compound Remember that some compounds and some clusters within a compound are more sensitive than others to pH changes and other matrix effects e Setting default transform windows and clearing transform windows described above for single clusters can also apply to multiple selected clusters Related Topics Add Peak on page 81 e Selecting Peaks and Clusters on page 82 e Adjusting Peaks on page 83 e Grouping Peaks as a Cluster on page 84 e Cluster Navigator on pa
205. on the size ofthe window on your screen in pixels If adjusting combinations of your window size and screen resolution do not let you produce images of a high enough quality consider using Export Spectrum Image Related Topics e Spectrum View Tools on page 20 e Export Spectrum Image on page 23 e Display Options on page 24 4 13 Display Options There are a number of ways in which you can customize modules in Chenomx NMR Suite to display information as you prefer You can toggle the display of graph elements in the Spectrum View and you can change scales You can find all ofthe following options in the View menu Table 4 2 View Menu Options X Scale Y Scale Sidebar Compound Sets Sidebar Legend Sidebar Processing History Sidebar Reference Panel Changes the units represented on the horizontal scale in the Spectrum View Available units are ppm and Hz Changes the units represented on the vertical scale in the Spectrum View Available units are si standardized intensity and ni normalized intensity Switches the Sidebar to the Compound Sets view Available in Profiler Switches the Sidebar to the Legend view Available in Processor Profiler Spin Simulator and Compound Builder Switches the Sidebar to the Processing History view Available in Processor Switches the Sidebar to the Reference Panel view Available in Profiler and Compound Builder 4 12 Copy Spectrum Im
206. ounds profiled or you have chosen to include compounds with no concentrations Related Topics Reference Panel on page 18 Spectrum View Tools on page 20 Compound Table on page 46 Starred Compounds on page 50 Quick Searches on page 50 Transforms on page 53 Maximum Concentrations on page 56 Scale Concentrations on page 57 Compound Set Tools on page 59 Export Profiled Data on page 60 Reference Panel Sidebar on page 65 Concentration Units on page 66 Transforms The frequencies of clusters ina compound signature that you are using may be different from those in the actual spectrum due to changes in solution pH ion concentrations and other matrix effects Transforms let you move the clusters from their starting locations to compensate for these effects and better fit the spectrum Transforms are normally limited to regions called transform windows Profiler displays the transform window for a particular cluster as triangles on the spectrum baseline when the cluster is selected You can move clusters beyond these limits if necessary 6 3 Profiling Tools 53 evomx CHENOMX NMR SUITE USER MANUAL How do I set transforms T Select a compound in the Compound Table If you do not see any compounds in the Compound Table select additional compound sets or use Quick Searches to find one Click and drag the blue triangle for a cluster along the horizontal
207. ounds to help ensure a consistent analysis or you may want to profile only specific compounds and cannot easily define rules that select the compounds you want Compound Sets let you include arbitrary compounds on a per compound basis hand picking the members of the set to suit your needs Although Compound Sets do not automatically include new compounds that you add to your library some changes to the library still affect Compound Sets If you remove a compound from the library or replace a compound with a new version the removal or update affects both Compound Sets and Smart Compound Sets How do I create an new empty Compound Set 1 Click New Compound Set 2 Enter a name for the new Compound Set 3 Start adding compounds from your library or other compound sets How do I create a new Compound Set containing specific compounds 1 Select a compound or group of compounds in the Compound Table 2 Click New Compound Set 3 Enteraname for the new Compound Set How do add compounds to an existing Compound Set 1 Selecta compound or group of compounds in the Compound Table 2 Click e g Add to My Compound Set to add the compounds to an existing set called My Compound Set Alternately drag the selected compounds onto the name of the Compound Set in the Compound Sets view How do remove compounds from a Compound Set 1 Selectthe Compound Set from which you would like to remove compounds in the Compound Sets view
208. ower and upper limits for the selected cluster Click OK How do I set the default transform window for a cluster Compound gt Transform Window gt Set Default on Selected Clusters z Menu Location Icon s Compound gt Transform Window gt Set Default on All Clusters E Menu Location Icon s 1 2 Select the cluster for which you would like to set the transform window On the Compound menu select Transform Window Set Default on Selected Cluster How do I set the default transform window for all clusters 1 On the Compound menu select Transform Window gt Set Default on All Clusters 8 3 Building Tools 87 evomx Compound gt Transform Window gt Clear for Selected Clusters Icon s ba Menu Location Compound gt Transform Window gt Clear for All Clusters Icon s ba Menu Location CHENOMX NMR SUITE USER MANUAL How do I clear the transform window for a cluster 1 Select the cluster for which you would like to clear the transform window 2 Onthe Compound menu select Transform Window gt Clear for Selected Clusters How do I clear the transform windows for all clusters 1 Onthe Compound menu select Transform Window gt Clear for All Clusters Tips and Tricks e When you set the transform windows for a cluster you can use mathematical expressions instead of constants to set the maximum and minimum values A special ic
209. ownfield top center A negative residual peak on the left suggests the cluster should be moved right or upfield bottom center Both identity and quantity can be considered reliable in the accurate profile far right Sum Line You will encounter situations in which the cluster you need to profile overlaps one or more clusters from other compounds regions fitting this description are often called busy regions You often need to profile compounds that have overlapped clusters in groups ensuring that the combined shape sum line matches the spectrum line First identify likely compounds contributing to the overlapped region Where available use non overlapped peaks including those in other regions of the spectrum to establish concentration ranges for the identified compounds Use partially exposed peaks to establish positions for each of the overlapped clusters Starting with the approximate shape thus obtained fine tune the position and height of each of the overlapped clusters to optimize the overall shape in the region Generally profile multiplets before singlets in overlap regions as they are easier to position accurately If all of the clusters for a compound are in overlap regions the profile may be unreliable especially if most or all of the clusters are low intensity singlets Overlap Region Contributing Compounds 1 Serine 2 Glycolate 3 Pantothenate AN Ny Fo 1 nd ll li Nf TY S JU
210. port Profiled Compounds Related Topics e Add Compounds on page 97 e Compound Set Tools on page 100 Send to Compound Builder Library Manager can help you to manage building and maintaining of your custom compound signatures You can send any compound visible in the Compound Table to Compound Builder for modifications When you save your changes you can add the modified compound to your library How do I send a compound to Compound Builder Menu Location File gt Send to Compound Builder 1 Select a compound in the Compound Table fon E 2 ClickSend to Compound Builder Hotkey s Eo 3 Make any desired changes to the compound signature in Compound Builder md 4 Savethe changes in Compound Builder 5 Close Compound Builder or close the file Tips and Tricks e Make sure that you have the Version column turned on in the Compound Table so you can see which compounds you have modified recently e You can send multiple compounds to Compound Builder by selecting them in the Compound Table right clicking on your selection and selecting Send to Compound Builder e You can only open five Compound Builder windows at the same time If you try to send more than five compounds to Compound Builder only five of them open and an error message appears indicating that the remaining compounds could not be opened Related Topics e Chapter 8 Compound Builder on page 77 e Compound Table on page 96 e Quick Searches on page 9
211. pounds In the absence of specific information about the behavior of a cluster you can set a default transform window for the cluster The default transform window is 0 006 ppm wide centered on the current cluster center For a cluster appearing at 1 000 ppm the default transform window sets lower and upper limits of 0 997 and 1 003 ppm respectively How do set pH sensitive transform windows Menu Location Tools gt pH Sensitivities e Icon s 1 2 3 On the Tools menu click pH Sensitivities Click Load Data Points Select the signatures that you would like to use to describe pH sensitive centers and transform windows for the compound Click Set Data Points Click Optimize Lines Review the clusters in the compound Click Accept to apply the automatically generated expressions for cluster centers and transform windows to your compound How do I set the transform window for a cluster Compound gt Transform Window Menu Location gt Edit for Selected Cluster Icon s Select the cluster for which you would like to set a transform window Open the Edit Transform Window dialog Select Limit transforms to and enter the new lower and upper limits for the selected cluster Click OK How do I change the transform window for a cluster 1 2 3 4 Select the cluster whose transform window you would like to change Open the Edit Transform Window dialog Enter the new l
212. ppm apart Related Topics Spectrum View Tools on page 20 Table 4 3 Preferences Overview General Preferences Internet Preferences Lets you configure Chenomx NMR Suite to access the Zooming Preferences Lets you change the color ofthe zoom box and toggle the Internet through a proxy server if needed or to disable connecting to the Internet entirely zooming animations used when you change zoom settings in the Spectrum View Graph Preferences Show Spectrum Line Toggles the default display of the spectrum line in the Show Sum Line Toggles the default display ofthe sum line in the Spectrum View in Profiler and lets you set its default color Show Compound Line Toggles the default display ofthe compound line in the Show Simulation Line Toggles the default display of the simulation line in the Spectrum View in Processor and Profiler and lets you set its default color Spectrum View in Compound Builder and lets you set its default color Spectrum View in Spin Simulator and lets you set its default color 4 14 Preferences 26 CHENOMX NMR SUITE USER MANUAL Show Subtraction Line Selection Line Overlay Lines CSI Line Processing Tools Initial Zoom ppm Toggles the default display ofthe subtraction line in the Spectrum View in every module except Library Manager and lets you set its default color Changes the default color of the selection line in the Spectrum View in P
213. presentative holders and should be noted as such viii Chapter 1 Introduction Welcome to Chenomx NMR Suite Before you begin analyzing spectra with Chenomx NMR Suite you need to install and activate the software 1 1 Installation Chenomx NMR Suite requires a Java Runtime Environment JRE Please download and install the latest version of Java from Oracle http java com The Windows installers for Chenomx NMR Suite will install a JRE automatically unless you already have a more recent JRE installed For Mac OS X you must have atleast OS X 10 5 Leopard installed on a 64 bit Intel Macintosh and install the latest version of Java supplied by Apple http www apple com After installing the software you need to activate it Please see Activation and Licensing on page 2 for more details Windows 32 bit 1 Runthe installer named ChenomxNmrSuite 7 0 windows setup x86 exe 2 Follow the instructions displayed on screen 3 You have now installed Chenomx NMR Suite Windows 64 bit 1 Runtheinstaller named ChenomxNmrSuite 7 0 windows setup x86 64 exe 2 Follow the instructions displayed on screen 3 You have now installed Chenomx NMR Suite Mac OS X 1 Open the DMG file named ChenomxNmrSuite 7 osx dmg 2 Dragand drop the Chenomx NMR Suite folder to your desired installation location 3 You have now installed Chenomx NMR Suite Linux 32 bit 1 Copy the installer script named ChenomxNmrSuite
214. pt automatic pH detection If the pH is not detected it will be set to 7 00 you can change it manually after the spectrum is imported Specify a pH value manually subject to the specified uncertainty Useful if your sample does not contain any of the pH indicators Access advanced import options Restore all import settings for the current file type to their default values Advanced Options Line Broadening Hz Zero Fill To Phasing Varian only Auto Phasing Delete Water Region 4 3 Saving Files Auto Baseline Correction Apply an exponential FID weighting line broadening function to your data You can enter any value between 0 and 1000 Hz Enable zero filling Automatic zero fills to the nearest power of two that is at least twice as large as the number of points acquired in your spectrum You can also choose a specific number of data points if you prefer Automatically apply phase adjustments to your spectrum Auto applies automatically determined phase angles while Import VNMR Phasing imports the phase angles found in the Varian procpar file Only available when you import Varian raw data fid Apply automatically determined phase angles to your spectrum Only available when you import non Varian raw data Automatically apply baseline correction to your spectrum Linear Drift applies a simple two point linear baseline correction while Spline applies a cubic spline baseline correction based on
215. r profiling efforts In many cases the number of compounds that could be contributing to a specific region of the spectrum can be large so it can be helpful to know some compounds that are more likely to be present If you do not have such alist and are expecting to analyze samples of a particular type on a regular basis you may find it helpful to develop a list of your own based on representative samples For the Profiler sample files the following compound list guided the profiling process 2 Oxoglutarate DSS Chemical Shape Indicator Pyruvate 3 Indoxylsulfate Formate Serine 4 Hydroxy 3 methoxymandelate Fucose Taurine Acetate Fumarate Threonine Alanine Glycolate Trimethylamine Citrate Niacinamide Urea Dimethylamine Pantothenate If you have a list of compounds common to a sample type you may want to create a Compound Set in Library Manager and use it to perform initial profiles of the spectra in your dataset Test Mixtures As you profile a series of spectra in a larger dataset you will notice that the profiling some mixtures of compounds is difficult You may want to try running controlled test mixtures of the compounds in question to establish their behaviour under your experimental conditions and use information from the test mixtures to guide your profiles of the larger dataset Test mixtures will help increase confidence and consistency in your profiling results Profiling Clusters Once yo
216. r setting a minimum transform window on clusters that do not move much with pH The general form of the cluster center operation is transformWindow ph n pkal pkaN shift1 shiftN 1 upper errorPh minDeltaPpm x extremal extremax where e The first four parts are the same as for the cluster center operation e upper is non zero true if you want the operation to return the upper bound of the calculated transform window and zero false if you want the lower e errorPh is the maximum amount of pH error to incorporate into the calculated transform window e minDeltaPpm is the minimum distance in ppm between the unmodified cluster center and the cluster center at ph errorPh or the minimum size of one half of the transform window e xis the number of extrema that the clusterCenter function represented in the first 5 arguments has e extremal extremaxthe extrema locations in pH ofthe clusterCenters extrema points There must be x of these but x may be zero The following expression is an example of a valid use of the transform window operation transformWindow ph 3 0 6902281 6 851296 9 289176 4 3607736 0 9786361 0 9779636 0 9253154 0 0 5 0 02 0 The above example refers to the same cluster as the cluster center example above The expression calculates the lower transform bound ofthe cluster since upper 9 subject to a pH error of 0 5 and a minimum distance of 0 02 ppm with no
217. rary Manager serves a different purpose from the one in Profiler The most obvious difference is that concentrations maximum or otherwise are not available in Library Manager since you are not profiling spectra More generally the Compound Table displays compounds in your library and lets you modify them When you first open Library Manager the Compound Table displays all of the compounds in your library As you select Compound Sets the Compound Table updates to reflect the contents of the currently selected set You can use the Compound Table to help you build Compound Sets via drag and drop and context menus You can also use text based Quick Searches to filter any list currently visible in the Compound Table There are many columns available for display in the Compound Table You can choose to display any number of the available columns with a minimum of one visible at any time and you can drag the column headers to position the columns in any order that you like You can sort the Compound Table on any column by clicking its column header Click the header again to reverse the sort order Tips and Tricks e You can add more compounds to a Compound Set by dragging them from the Compound Table onto the name of the Compound Set or by right clicking on the compound and selecting Add to New Compound Set or Add to You cannot add compounds to Smart Compound Sets directly e You can edit a compound in the Compound Table by right clicking on
218. raw spectrum file using either the included Processor module or one of the following software packages e VNMRand VNMRj Varian phasefile files e XWIN NMR Bruker 1r files e Delta JEOL jdf files e NMRPipe ft2 files 2 2 Spectral Data Acquisition 5 evomx CHENOMX NMR SUITE USER MANUAL e ACD Labs software package Export your spectra to the JCAMP DX format jdx files Zero Filling e To ensure maximum compatibility with the Chenomx Reference Compounds zero fill your data e When zero filling use the nearest power of 2 that is at least twice as large as the number of points acquired in the original spectrum e g for 16000 points in the original spectrum use zero filling of 32K points To do this in Processor select Automatic in the import dialog under zero filling Data Transformation e Donotapply any transformations like sine bell or Gaussian functions to your spectra Basic Processing Forthe bestresults you must properly phase and baseline correct all of your spectra Line Widths e For the best results your spectra should have CSI linewidths of no more than 1 5 Hz Use an appropriate combination of reference deconvolution and line broadening to adjust the linewidths Data Processed with Other Software If you would like to process your spectra using software packages other than the Processor module you need to ensure that the Fourier transformed frequency domain data from your processed spectra ar
219. rder phase angles until most peaks in the spectrum appear symmetrical The water peak often does not phase properly with the rest of the spectrum so focus on other signals in the spectrum instead Phase angles for the sample spectrum are near 54 zero order and 2 first order Click the Accept button to apply the changes to the spectrum and exit Phasing mode Applying Baseline Correction 8 9 10 11 12 13 Switch to Baseline Correction mode Click the Auto Linear button to have Processor locate the spectrum endpoints automatically The automatic linear baseline correction provides a useful starting point for the more involved spline correction Click the Auto Spline button to have Processor place an initial set of breakpoints on the spectrum for you Click in the spectrum viewing pane to add more breakpoints for a cubic spline baseline fit Use more points where the baseline is strongly curved and fewer points where it is more linear Breakpoints normally appear on the spectrum line Hold down the Control or Command key while clicking to place breakpoints at arbitrary positions Continue placing breakpoints until the blue line follows the spectrum baseline as closely as possible When you are satisfied with your fit of the spectrum baseline click the Accept button to apply your changes to the spectrum Adjusting the CSI Settings 14 15 16 17 Switch to the CSI Editor Zoom in on the si
220. re the same as those found in the unbounded cluster center operation see Cluster Center on page 138 The following expression is an example of a valid use ofthe bounded cluster center operation bClusterCenter 4 07 9 02 ph 3 0 6902281 6 851296 9 289176 4 3607736 0 9786361 0 9779636 0 9253154 The above example describes the same cluster as in the cluster center example see Cluster Center on page 138 now subject to a pH range of 4 07 to 9 02 The general form of the bounded transform operation is bTransformWindow lowerBound upperBound ph n pkal pkaN shift1 shiftN 1 upper errorPh minDeltaPpm x extremal extremax where e lowerBoundis the lowest pH at which the operation is considered valid e upperBoundis the highest pH at which the operation is considered valid e The remaining arguments are the same as those found in the unbounded transform window operation see Transform Window on page 138 The following expression is an example of a valid use ofthe bounded cluster center operation bTransformWindow 4 07 9 02 ph 3 0 6902281 6 851296 9 289176 4 3607736 0 9786361 0 9779636 0 9253154 0 0 5 0 02 0 The above example describes the same transform bound as in the unbounded transform window example see Transform Window on page 138 now subjectto a pH range of 4 07 to 9 02 10 9 Using Expressions 140 Glossary 1r A acquisition time activation adding co
221. reate Smart Compound Sets based on sets of rules that select compounds from your library Smart Compound Sets automatically update to reflect changes in your library If you add new compounds to your library they immediately appear in any Smart Compound Sets with rules that match the new compounds Simple rules might be all compounds that I can use to profile 800 MHz spectra or all compounds with acetate in their names However you can also use Smart Compound Sets to select all compounds useful for profiling 600 MHz spectra with a valid pH range from 5 54 to 8 39 added to the library after January 1 2010 with a molecular weight less than 300 g mol and whose name starts with the letter a You can be as specific or as general as you like You can also quickly merge results from existing Compound Sets selecting compounds that are in Set A but not in Set D Smart Compound Sets can help you focus on just the compounds that you are interested in without having to worry about updating the sets as you add new compounds to your library or update existing compounds How do I create a new Smart Compound Set 1 Openthe New Smart Compound Set dialog 2 Enteraname for the new Smart Compound Set 3 Enterthe desired magnet frequency for the Smart Compound Set 4 Use the drop down menus to define any additional search filters that you would like to apply to the Smart Compound Set Use the buttons to add new filters 5 Click OK Ho
222. remain intact Undo Redo Zoom Menuilocation View gt Zoom gt Undo Redo Zoom Just as Undo and Redo let you recall recent actions Undo Zoom and Redo Zoom let you one A 2 recall recent views of the spectrum Hotkey s or Tips and Tricks e You can access up to twenty recent views through Undo Zoom e Redo Zoom is not available until you have used Undo Zoom at least once 4 10 Spectrum View Tools 20 nom View gt Zoom gt Auto Zoom Icon s P Ctrl F Menu Location Hotkey s md View Zoom Increase Decrease Vertical Zoom tf plus or minus Menu Location Icon s Hotkey s View Zoom Menu Location Increase Decrease Horizontal Zoom Icon s a e Hotkey s asterisk or slash CHENOMX NMR SUITE USER MANUAL Auto Zoom Auto Zoom lets you quickly adjust the vertical scale of the current view so that the tallest peak in the currently displayed frequency range fits in the viewing pane without changing the displayed frequency range Tips and Tricks e You can apply Auto Zoom to the Spectrum View at any time by clicking anywhere on the spectrum with the middle mouse button Increase Decrease Vertical Zoom Increase Decrease Vertical Zoom lets you incrementally adjust the vertical scale ofthe current view without changing the displayed frequency range Tips and Tricks Decrease Vertical Zoom is not available when the full int
223. rentzian peaks corresponding to energy transfer among spins in a spin system The result ofa simulation in Spin Simulator is a series oftransitions the sum of which is the simulation line red Abbreviation of 3 trimethylsilylpropionate a CSI supported by Chenomx NMR Suite as an alternative to DSS The chemical shift of TSP is sensitive to pH In Spin Simulator a J modifier that splits a spin definition as though it were coupled to a number of protons equivalent to the spin count by an amount equal to the specified J value in Hz Standard identifier commonly used in software to identify a piece of information like a compound signature in such a way that the same identifier is never used for another piece of information 154 CHENOMX NMR SUITE USER MANUAL ENOMX unprocessed spectrum Spectrum data stored as it was recorded by the spectrometer data with no modifications UUID See universally unique identifier valid pH Optional parameter describing the pH at which a compound signature is expected to accurately reflect an experimental spectrum Often correlates with the pH range used to determine transform windows vertical zoom Adjusts the scale of the Spectrum View in the vertical direction without changing the displayed frequency range VNMR Older NMR software package developed by Varian to run their spectrometers and process the resulting data VNMRj NMR software package developed by Varian to run their spectrom
224. rofiler Compound Builder and Spin Simulator Changes the default color of spectrum overlay lines in the Spectrum View in Profiler Processor Compound Builder and Spin Simulator Changes the default color ofthe CSI line in the CSI Editor s Spectrum View in Processor Changes the default color of the processing tools in Processor including the baseline correction breakpoints reference deconvolution peak adjustment triangles etc Sets the frequency range of the Spectrum View that initially appears when you open a file File Preferences Display Recent Files Default File Folder Sets the number of files displayed when you click File then Open Recent Sets the default folder for saving and opening files Options are to use the last used folder or always use the specified folder 4 14 Preferences 27 Chapter 5 Processor The Processor module lets you convert spectra into the Chenomx NMR Suite format cnx and perform basic processing Currently Processor can import raw data in Varian fid Bruker fid JEOL jd f and NMRPipe fid formats and processed data in Varian phasefile Bruker 1r JEOL jdf NMRPipe ft2 and JCAMP DX jdx formats Regardless of the source format Processor saves spectra as spectrum files cnx 5 1 Overview Processing History m 1 Phasing igh 2 Baseine Correction M gt
225. rs for the current compound overlap with compounds that you have already profiled you may need to readjust those compounds 3 5 Determining Compound Concentrations 12 Chapter 4 The Basics Menu Location Icon s Hotkey s File Open Ctrl O Cmd O Chenomx NMR Suite includes many advanced features that help you process and analyze spectra create custom compound signatures and manage compound signatures and compound sets in your library Underlying all of these advanced features is a set of more basic ones that are fundamental to the proper use of Chenomx NMR Suite The basics include file operations navigation display options and preferences that directly affect your day to day use of Chenomx NMR Suite 4 1 Opening Files You can open and overlay Chenomx NMR Suite spectra cnx in Processor and Profiler and overlay them in Compound Builder and Spin Simulator You can open Chenomx compound files xcpd in Compound Builder and you can open Chenomx spin simulation files xss in Spin Simulator and import them in Compound Builder How do open a file 1 Opena module 2 Openthe file selection dialog 3 Locate the folder containing the spectrum 4 Selectthe file and click Open 5 If the file you are opening requires importing select import options as necessary Tips and Tricks e Ifyou are opening a Varian spectrum named Example fid the raw data is stored in the file named Example fid
226. rticular compound or group of compounds 6 1 Overview 43 Enom CHENOMX NMR SUITE USER MANUAL Spectrum Thumbnail Displays a thumbnail image of the current spectrum You can also use the thumbnail to navigate the Spectrum View at various zoom settings Status Bar Displays the current cursor position in the units specified by the View gt X Scale and View gt Y Scale settings Also displays information about recent user actions 6 2 Quick Reference Guide Linux Windows Mac OS X File Menu Open Ctrl O Cmd O Open Recent sae Close Ctrl W Cmd W L3 Save Ctrl S Cmd S Save As gss 2 Send to Processor Ctrl J Cmd J B Open Library Manager Ctrl B Cmd B g Import Profile S3 Export gt Profiled Data txt b Export gt Profiled Compounds pack m Export Spectrum Image gre 3 Spectrum Details A Preferences zes Exit cae Edit Menu A Undo Ctrl Z Cmd Z Redo Ctrl Y Cmd Y m Copy Spectrum Image to Clipboard Enforce Transform Windows Ctrl Shift X Cmd Shift X View Menu Concentration Units X Scale Y Scale 6 2 Quick Reference Guide 44 CHENOMX NMR SUITE USER MANUAL Enom Linux Windows Mac OS X lel Zoom Show Entire Spectrum Ctrl Minus Cmd Minus M Zoom Undo Zoom R Zoom gt Redo Zoom Zoom Set Zoom Ctrl M Cmd M HT I Zoom Select Region Ctrl T C
227. rties including cluster centers and transform windows These expressions allow compounds to partially adapt to the spectrum before you profile it reducing the time and effort needed to accurately identify compounds in the spectrum Before you can create a pH sensitive compound for your Library you will need some data to work with Preparing to create a pH sensitive compound 1 Prepare one signature file to be made pH sensitive the master signature You can use the valine signature file that you created in the Compound Builder tutorial see Simple Compound Valine on page 129 as a starting point 2 Prepare a number of other signature files partial signatures spanning the pH range over which you would like your pH sensitive compound to be valid For each of these e Set the valid pH to the pH of the original sample e Make sure each partial signature has the same number of clusters in the same order as the master signature Rearrange the cluster IDs if necessary see Manage Cluster IDs on page 90 e Make sure that the cluster centers in each partial signature are as accurate as possible as these will be used along with the pH values to generate the necessary expressions Building a pH Sensitive Compound Once you have built the necessary signatures turning them into a pH sensitive compound signature is quite simple Remember that the quality of the pH sensitive signature that you build is directly related to the
228. s open the spectrum in Processor and use the pH editor The value that you setin the pH editor appears in the exported file when you choose spectrum pH values as extra data to export Use the default layout to export files that you intend to open with statistical analysis packages Use the transposed layout to export files that you intend to open in a spreadsheet program or if you prefer the transposed layout If you intend to open the exported file in Microsoft Excel 2003 or earlier limit the number of compounds to less than 253 for the Default layout or the number of files to less than 253 for the Transposed layout since these versions of Excel do not support large numbers of columns Related Topics Profiling Tools on page 46 Compound Set Tools on page 59 Concentration Units on page 66 Export Profiled Compounds When you collaborate with other people on a project you may have different compounds in your library than your collaborator has in theirs Exporting profiled compounds creates a compound pack pack containing the set of actual compound signatures that you used to fit spectra for the project You can exchange compound packs with other users of Chenomx NMR Suite and import new packs via Library Manager You can then be certain that you and your collaborator are always profiling spectra for that project using the same collection of compound signatures How do export a compound pack from the current spe
229. s a Cluster on page 84 Optimize Selected Peak Shapes on page 85 Generate Cluster for Region on page 86 Transform Windows on page 86 Cluster Navigator on page 90 Information Panel on page 92 Using Expressions on page 135 Grouping Peaks as a Cluster During the building process and especially when you are building more complex compounds you may need to group peaks from one or more clusters into a cluster oftheir own Grouping 8 3 Building Tools 84 evomx Menu Location Icon s Hotkey s Compound Group Selected Peaks as Cluster Ctrl G Cmd G Menu Location Icon s Hotkey s Tools Optimize Selected Peak Shapes CA Ctrl I Cmd l CHENOMX NMR SUITE USER MANUAL ensures that all ofthe selected peaks move together when you use the compound signature for profiling and that they obey the same transform window settings How do I group peaks as a cluster 1 Selectthe peaks and clusters that you would like to group as a new cluster 2 Click Group Selected Peaks as Cluster Tips and Tricks e Right click on a selection in the Spectrum View or Information Panel and select Group Selected Peaks as Cluster to group the selected peaks directly e After grouping peaks into a new cluster you may want to use the Edit Selected Peaks dialog to set them all to a common width Related Topics e Add Peak on page 81 e Selecting Peaks and Clusters on page 82 e Adjust
230. sdisenacens 8 3 2 Profiling Spectrum eee dein een ERREUR ee e da puru deena 8 3 3 Identifying Compounds neon niea nie a emer bl AEE Ene TE reda 9 3 4 Profiling Overlapped Regions in a Spectrum sseseeeense 11 3 5 Determining Compound Concentrations sseseenmm 11 4 The BASICS uec eth eter PF E e a rax E UR EEad rai AY Ebo sw ctvR EEE Ede toL ERE stances 13 A TO pening PiuleSivesscssdttecndcecnecciedcxecndenteecdiadennaddveaxaaniedikastdesimenseteddeeakdsuareances 13 4 2 Importing Spectra srein ienes Eeo EEE EESE SEET iei 13 DESEAS MURAT 14 AA Closing Files REPE HI DE PU M ead 15 Ais Exiting Modules irissen eet tend ne eh dsuaveencoddeds AARE AREE E 15 4 6 Undo and Redo rite tiro E o Ra kk eu EPA LER EXE KPuRP REED d Eei 16 4 7 Change Columrmis tenni diete in e baee gene d t a a R EA xe dac TAA as ARUM 16 4 8 SIdeDar eiecti EE AE Eo FEE EUR TAKE ERR ES Hs E ERES Euer E Er cere 16 Legend eta tenaci specus a seres EA T A 17 Reference Panel iiiiicisics TEE 18 Processing HIStOLY ssiiisaccccssvescaaccresnaess cancetandedcadtenstudenedacsea sax Dae s EA dx daas 18 opm nori c r 18 junuicoM Uani ieni 19 4 9 Spectrum Overlays risos De ea e pee ide i Dele te uH 19 4 10 Spectrum View Tools cie teint cione abesenocku xem reni deaxi d ki Alei vecRre i cue Ens 20 Show Entire Spectrum iiec rer ne E EE ter ener gto MERE us 20 MA Tug
231. se file types then click Choose Files Click Next If you like choose how you would like compound sets created Click Finish to add the selected compounds 9 3 Library Tools 97 evomx CHENOMX NMR SUITE USER MANUAL Tips and Tricks When you add compounds any compound sets that were created or modified during the addition process throb for a couple seconds to indicate which sets were affected by the import The addition process will not create duplicate Compound Sets If the addition options that you selected would normally create a Compound Set with the same name as an existing set the existing set will be updated with the added compounds Related Topics Compound Table on page 96 Compound Set Tools on page 100 Export Compounds When you collaborate with other people on a project you may have different compounds in your library than your collaborator has in theirs Exporting compounds allows you to exchange compound signatures with other users of Chenomx NMR Suite You can then be certain that you and your collaborator are always fitting spectra for that project using the same set of compound signatures You can export compounds as a single compound pack file pack or as collections of individual signature files xcpd How do export compounds to a compound pack Menu Location Icon s Compounds Export Selected Compounds to Compound Pack pack 7 1 2 3
232. see Water Suppression on page 120 Clear the quick search box Click Show Entire Spectrum Profiling the Remaining Compounds 25 Using the techniques discussed above profile the remaining nine compounds in the spectrum You can check your results for all of the compounds with the following list of concentrations If you are unsure what the finished profile should look like open the file Basic End cnx to view this spectrum with profiling completed Note that in one instance 3 indoxylsulfate Profiler is unable to suggest a concentration or transforms via Fit Automatically due to the atypical shape of the cluster at 7 3 ppm For this compound choose a concentration that provides the best match to the other clusters then adjust frequencies of each cluster to best match the spectrum Some clusters are more reliable than others when determining concentrations of compounds that have multiple clusters When you determine concentrations manually use clusters 10 3 Profiler 111 evomx CHENOMX NMR SUITE USER MANUAL meeting as many of the following criteria as possible to set the concentration for such compounds e Minimal overlap Ideally the cluster should have no other clusters overlapping e More protons If a cluster corresponds to three protons such as a methyl group the signal for that cluster is stronger than the signal for a cluster corresponding to only one proton e Unobscured If a cluster appears
233. selection line in the Legend 1 Switch to the Legend view in the Sidebar 2 Selecta compound in the Compound Table 3 Click the red pin 4 appearing beside the selection line How do I make a pinned compound active using the Legend 1 Switch to the Legend view in the Sidebar 2 Clicka pinned compound in the Legend view Tips and Tricks The compound currently selected in the Compound Table will always appear in the Legend as the selection line e You can adjust the display of compound lines through the Legend view in the Sidebar including setting custom colors pinning compounds and selecting a compound for use in profiling Related Topics Legend on page 17 e Compound Table on page 46 e Custom Colors on page 48 e Pinned Compounds on page 49 Reference Panel Sidebar The Reference Panel Sidebar view displays information specific to the compound that you View Sidebar Reference have selected in the Compound Table This includes a structure image molecular formula Panel and weight alternate names and links to external reference sites You can use this information to verify the identity ofthe compound that you are fitting and better understand the signature Menu Location Icon s ep and behaviour of the compound in your spectra Ctrl Shift R Pere Vis eo Tips and Tricks You can open the Reference Panel for a specific compound by double clicking the compound in the Compound Table
234. st be profiled using this technique the profiled compound both identity and quantity should be considered unreliable 0 06 O Phosphocholine 35 uv Clusters 3 and 4 0 04 0 02 PR oe pr A 0 06 0 04 I 0 02 f 0 00 gt T T m T T T T T 4 26 4 24 422 420 4 18 4 16 4 14 4 12 Figure 10 9 The large cluster near 3 2 ppm was sufficient to establish the identity and quantity of O phosphocholine Although there are no obvious peaks that can be used to align clusters 3 and 4 top it seems reasonable to move them over to fit more neatly under the nearby hump in the spectrum bottom No Fit When profiling some compounds you may find that a cluster is not visible in the signature or the spectrum or both at concentrations consistent with the spectrum Since no information is available to help you profile the cluster the best course is to leave the cluster at its starting position If all of the clusters for a compound fall into this category the compound should be considered not detected in the sample 10 4 Targeted Profiling 121 ENOMX CHENOMX NMR SUITE USER MANUAL Isoleucine 9 uv Cluster 0 right Cluster 1 left 0 04 0 03 a f MA f ooi MA l l AC Ww f VIR yr We Wl SNP EV ues gt r lt gt A 4 1 00 0 95 0 90 T 0 00 Figure 10 10 The doublet near 1 ppm provides enough information to set a concentration for iso
235. t 84 cluster selection 93 compound table 47 concentration 52 CSI peak 31 display next cluster 58 84 display previous cluster 58 84 horizontal scroll 21 peak adjustment 84 peak selection 93 phasing 36 select by cluster 82 select by peak 82 select region 22 spectrum pH 33 spin definition 72 transform 54 zoom 21 L legend sidebar 17 64 library manager open 59 license file cnxlic 2 line broadening 38 line color 25 M magnet frequency 91 manage cluster IDs 90 maximum concentration 56 N new compound 80 compound set 101 simulation 70 smart compound set 102 157 Enom next spin definition 72 NMR parameters acquisition time 5 relaxation delay 5 spectral width 5 temperature 5 NMRPipe processed data ft2 13 spectrum file fid 13 no fit 121 normalization 62 0 optimize selected peak shapes 85 output options 62 overlay spectrum 19 overview Compound Builder 77 Library Manager 94 Processor 28 Profiler 43 Spin Simulator 67 P peak add 81 delete 83 edit 83 group as cluster 84 list 92 optimize selected 85 select 82 pH creatinine 4 8 32 DFTMP 4 8 32 editor 32 find automatically 32 imidazole 4 8 32 indicator 4 internal standard 4 sensitivities 88 spectrum 32 uncertainty 8 pH sensitivities 88 phasing automatic 36 first order 36 zero order 36 pin 46 49 portable document format pdf 23
236. t will let you verify that the compound is present in a spectrum without necessarily providing the full range of flexibility that a chemically accurate signature affords You can create these limited use signatures using automatically generated clusters Generated clusters lack the chemical accuracy of signatures that are backed by spin simulations but provide a quick model of the lineshape of a compound under specific conditions How do generate a cluster to match a region of the spectrum 1 Selectthe region ofthe spectrum that you would like to match with a generated cluster 2 Click Generate Cluster for Region Tips and Tricks e Generated clusters have no formal theoretical basis They simply add a number of Lorentzian peaks that approximate the overall shape ofthe spectrum in the selected region The generated peaks will notlet you accurately account for significant changes in the spectrum based on magnet frequency pH or other systematic variations e Signatures based on generated clusters may only be expected to give accurate results when profiling spectra acquired under conditions very similar to the source spectrum Generated clusters are already optimized Further optimizations will not generally give any better results e When you generate a cluster Compound Builder will only use up to 100 peaks to match the selected region If the region you are trying to match cannot be accurately modeled using 100 peaks try selecting
237. tch reasonably well see Cluster Navigator on page 58 If all clusters appear reasonably well matched apply an automatic fit then adjust the concentration and transforms for the compound as needed see Concentrations on page 52 Transforms on page 53 and Fit Automatically on page 55 If the shape does not appear reasonable continue evaluating the remainder of the compounds in the list When you have finished with the filtered list clear the frequency filter to continue your analysis with the full compound list see Quick Searches on page 50 3 3 Identifying Compounds 10 evomx CHENOMX NMR SUITE USER MANUAL 3 4 Profiling Overlapped Regions in a Spectrum For all but the simplest spectra you need to profile compounds whose signatures overlap Approaches to profiling these overlap regions are as varied as are the number of people profiling them but the general guidelines below may help you to develop your own strategy As with your more general approach to profiling spectra a consistent strategy for profiling overlap regions gives you more consistent results For more details on this and other profiling strategies see Targeted Profiling on page 116 To profile compounds in an overlapped region of the spectrum 1 Identify likely compounds contributing to an overlapped region see Identifying Compounds on page 9 2 Evaluate each compound for the presence of additional non overlapped peaks elsewher
238. the Spectrum View as aordered list of the approximate positions of all the clusters of the compound in ppm When you click on a cluster position the view zooms to provide an optimal view of the cluster The optimal view includes the larger of the full transform range of the cluster or the full width of the cluster and the full vertical extent of any peaks within the horizontal range You can also use the Cluster Navigator to move sequentially through the list of clusters in either direction How do display the clusters of a compound in the Spectrum View Menu Location Hotkey s View Show Cluster Navigator Ctrl Shift N Cmd Shift N 1 2 Make sure that the Cluster Navigator is visible Clicka cluster position to zoom directly to that cluster Click the left or right arrow to move sequentially through the list of clusters Tips and Tricks Clusters that appear green in the Cluster Navigator are pH sensitive meaning that one or more of their heights positions and widths change with spectrum pH Click on a cluster and drag along the Cluster Navigator to include adjacent clusters in the Spectrum View 8 3 Building Tools 90 cH CHENOMX NMR SUITE USER MANUAL Related Topics e Add Peak on page 81 e Selecting Peaks and Clusters on page 82 e Adjusting Peaks on page 83 e Grouping Peaks as a Cluster on page 84 e Transform Windows on page 86 8 4 Information Tools While building compou
239. the acid dissociation constant of the indicator ml is a correction for ionic strength A6 is the chemical shift difference between the peaks and Amax and Amin are the upper and lower bounds on the chemical shift difference The single peak equation for DFTMP derives from a similar equation published recently see citation below The two peak equation was developed internally by Chenomx 5 3 Information Tools 32 evomx CHENOMX NMR SUITE USER MANUAL MD Reily LC Robosky ML Manning A Butler JD Baker and RT Winters 2006 DFTMP an NMR Reagent for Assessing the Near Neutral pH of Biological Samples Am Chem Soc 128 38 12360 12361 The predicted frequencies of the imidazole creatinine and DFTMP peaks based on the pH value that you currently have set appear in the Spectrum View as a pair of blue lines at high frequency imidazole a pair of green lines at mid frequency creatinine anda single orange line at low frequency DFTMP You can use these lines during manual pH determination by aligning them with the corresponding peaks for creatinine imidazole and DFTMP when these compounds are present How do set the spectrum pH Menu Location View gt Edit Mode gt pH Menu Location Icon s Tools Find pH Automatically 1 2 Switch to the pH Editor Set the desired pH using any one of the following methods e Click the Find Automatically button e Onthe Tools menu click Find pH Automa
240. the spectrum Right click on the selected region and click Filter for Compounds in Selected Region Click the red X at the right edge of the search box to cancel the search and restore the full list of compounds Filter Compounds is an alternate method for setting up a Quick Search based on a frequency or range that you type rather than based on clicked locations in the Spectrum View How do filter the compounds in the Compound Table based on a specific frequency Menu Location Icon s Tools Filter Compounds r or range 1 Openthe Filter Compounds dialog 2 Enterthe frequency or range that you want to use to filter the Compound Table 3 ClickOK Tips and Tricks Use Quick Searches to temporarily limit the number of compounds displayed Use compound sets created in Library Manager to define a more permanent working set of compounds for profiling a particular type of spectra You can click repeatedly anywhere under the sum line red in the Spectrum View to cycle through the compounds contributing to the sum line at the frequency that you clicked When you right click anywhere under the sum line red in the Spectrum View the resulting context menu shows a list of compounds contributing to the sum line at the frequency that you clicked Select a compound from the list to make it the active compound You can perform frequency and frequency range searches directly from the Quick Search box For example
241. thyl signal in that spectrum is 2 si since 1 00 mM is twice the standard concentration of 0 50 mM Refers to a linewidth relative to that of a theoretical DSS methyl peak at a concentration of 0 50 millimoles per litre mM In Profiler a compound for which you have toggled the Star column on yellow Line in the Spectrum View in Profiler Compound Builder and Spin Simulator showing the difference between the black line spectrum or overlay line and the red line sum compound or simulation line colored green by default Advanced profiling technique giving very accurate results For a subtraction line fit you manipulate concentrations and transforms fora compound so that the subtraction line green approximates anormal spectrum indicating that the influence of the compound has been efficiently subtracted from the original spectrum Line in the Spectrum View in Profiler representing the sum of all of the compound lines in the profile of the currently open spectrum colored red by default Profiling technique needed for fitting overlapped regions For a sum line fit you manipulate clusters overlapping in a particular region so that the sum line red in that region best approximates the spectrum line black Other clusters for the same compounds that occur in other potentially less overlapped regions will often contribute to this technique See scalable vector graphics See standardized width 153 CHENOMX NMR SUI
242. tically e Click and drag the pH slider bar to set the determined frequencies of imidazole creatinine and DFTMP as close as possible to the actual frequencies ofthe peaks in the spectrum if known The resulting pH appears in the text box beside the slider bar e Select the pH slider control and use the arrow keys to make fine adjustments to the pH in increments of 0 01 e Type the desired numeric pH into the text entry box to the right of the slider bar Tips and Tricks Settingan accurate spectrum pH helps Profiler choose more accurate starting positions and transform windows for clusters When aligning the displayed lines to peaks in your spectrum it is not necessary to have the lines match the peak positions precisely A common situation is to arrive at two pH values separated by 0 01 one of which places the indicator lines on one side ofthe peak while the other places them on the other side of the peak In such cases you may use either value Once you have made coarse adjustments to the pH you can zoom in to particular indicator lines to make finer adjustments Select the Fine Tune check box to let you make more detailed adjustments over a smaller pH range If you have selected TSP or formate as the CSI then changing the pH changes the position of the horizontal axis since the frequencies of the TSP and formate peaks are pH sensitive Processor must be in the pH Edit Mode to adjust the pH for your spectrum You must sav
243. tinine signal then the intensity of the urea signal is 0 5 ni In Compound Builder an operation that automatically adjusts the centers heights and widths of the selected peaks to match the spectrum overlay by minimizing the average intensity of the subtraction line Lines in the Spectrum View corresponding to spectra loaded for comparison to the currently loaded spectrum in Processor and Profiler the current simulation in Simulator or the current compound signature in Compound Builder See compound pack See portable document format Mathematical model ofa signal appearing in a spectrum Chenomx NMR Suite models all peaks as pure Lorentzian curves Mode used in Processor to determine the sample pH for a spectrum based on the approximate peak positions ofone or more pH indicators 147 evomx CHENOMX NMR SUITE USER MANUAL PH indicator phase correction phasefile phasing pinned compound pinned lines png portable document format portable network graphics preprocessing preview line Processing History processing layer Compound that you add a sample to let you detect the sample pH Indicators supported by Chenomx NMR Suite like creatinine imidazole and DFTMP have signals whose chemical shifts change with the pH of the sample Sample pH can thus be determined by measuring the signals chemical shifts See phasing Data from spectra processed using the VNMR or VNMRj software pa
244. tion log vii auto zoom 21 automatic baseline correction 37 fit single compound 55 phasing 36 B baseline correction automatic 37 breakpoint 37 frowns 37 rolling 37 smiles 37 wings 37 best guess fit 121 bin label 62 size 62 width 62 bin definitions 62 binning configuration file 62 binning target 62 breakpoint 37 Bruker processed data 1r 13 spectrum file fid 13 C change columns 16 chemical shift 4 Chenomx file types compound album file cca 80 compound file xcpd 13 80 compound pack pack 61 license file cnxlic 2 simulation file xss 13 70 80 spectrum file cnx 13 41 Chenomx Reference Compounds add 3 97 Reference Compound Sets 59 transform windows 55 Chenomx Technical Support vii clear concentration 52 transform 53 transform window 86 cluster generate for region 86 group peaks as 84 list 92 navigator 58 90 select 82 cluster IDs manage 90 comment 34 compound add to Compound Set 101 album file cca 80 author 91 details 91 file xcpd 13 80 filter in selected region 50 filter near x xx ppm 50 ID 91 magnet frequency 91 name 91 new 80 pack pack 61 pH sensitive 88 remove 99 remove from compound set 101 sample concentration 91 set 59 96 100 101 102 103 table 46 96 UUID 91 compound line fit 117 compound set edit 102 export compound files xcpd 98 export compound pack pack
245. trl Alt 6 Cmd Alt 6 Tools Menu ud Add Spectrum Overlays Ctrl Shift O Cmd Shift O m Remove All Spectrum Overlays J Find CSI Automatically X Find pH Automatically qa Convert Spectra Help Menu NMR Suite Help F1 F1 td Save Application Log Ctrl Shift A Cmd Shift A E Software Activation ees 9 About Chenomx NMR Suite 5 3 Information Tools In addition to processing the spectrum itself you can add extra information to a spectrum that lets you analyze the spectrum in Profiler or create compound signatures and simulations 5 3 Information Tools 30 CHENOMX NMR SUITE USER MANUAL in Compound Builder and Spin Simulator You can also review processing layers that you have added and remove them if necessary CSI Editor The chemical shape indicator CSI settings form the basis for all fits performed in Profiler and Compound Builder The accuracy of these settings also have a direct impact on the accuracy of profiled spectra cnx exported data txt compound files xcpd and spin simulations xss The CSI editor lets you view define and change these settings for the current spectrum When you import a spectrum Processor attempts to automatically locate the CSI and determine its width and height You can change these automatically determined parameters using the CSI editor if necessary How do I modify the CSI settings Menu Locat
246. trum Methyl groups can be very useful in setting an appropriate concentration for a compound as they are usually easy to locate 5 Use Fit Automatically press the space bar then adjust the concentration of pantothenate to match the spectrum in this region 6 Clickthelocation ofthe next pantothenate cluster 2 4 ppm in the Cluster Navigator 7 Adjust the frequency ofthe cluster to match the signature blue to the spectrum black Although the left most peak of this cluster overlaps with 2 oxoglutarate the remaining two peaks provide enough information to establish an appropriate frequency for the cluster It is good practice to completely finish fitting an overlap region before moving on to the next one Since the only other compound in this region is 2 oxoglutarate it is the next logical compound to consider 8 Inthe Compound Table select 2 oxoglutarate and use Fit Automatically 9 Adjust the 2 oxoglutarate cluster near 2 43 ppm as needed to match the spectrum Notice that the sum line red at 2 417 ppm now matches the spectrum more closely than it did with only pantothenate adjusted Since 2 oxoglutarate is quite simple you can finish profiling it before continuing with pantothenate 10 Movetothe remaining 2 oxoglutarate cluster 3 0 ppm using the Cluster Navigator and adjust the frequency of the cluster as needed to match the spectrum 11 Select pantothenate again 10 3 Profiler 113 evomx CHENOMX NM
247. ty spectra Pay particular attention to proper shimming phasing and baseline correction to produce spectra that you can accurately analyze and interpret using Chenomx NMR Suite Chenomx NMR Suite can automatically detect DSS or TSP signals in most spectra However automatic detection relies on the water peak being centered in the spectrum For best results ensure that the water peak is centered in your spectra Pulse Sequences Using Chenomx NMR Suite you can quantitatively analyze spectra produced by NOESY pulse sequences with t of 100 ms You can use other pulse sequences for identification purposes but quantification based on alternate pulse sequences may be unreliable Required NMR Parameters For the best results from Chenomx NMR Suite when analyzing your data use the following parameters for NMR data collection e Temperature 25 C e Acquisition time 4 s e Relaxation delay 1 s e Spectral width 12 ppm Tips and Tricks e Chenomx NMR Suite is capable of automatically detecting DSS in your spectra However automatic detection relies on the water peak in your aqueous 1H NMR spectrum being centered in the spectrum 2 3 Spectral Data Processing Chenomx NMR Suite can import raw data from a number of common sources Supported raw file formats include e Varian fid files e Bruker fid files e JEOL jdf files e NMRPipe fid files Toanalyze a spectrum with Chenomx NMR Suite you must first process your
248. u have selected a compound to profile you need to match the individual clusters of the compound in their respective regions of the spectrum There are several common approaches to profiling clusters and in a typical spectrum more than one method will be necessary Try to maintain a consistent approach to profiling spectra in a dataset as this will help you obtain accurate and consistent results from your analysis Compound Line The simplest way to match a cluster to a region of the spectrum is to adjust the cluster so that the compound line blue by default unless you have assigned custom colors matches the spectrum line black The compound line is most useful for isolated low intensity clusters If you profile all of the clusters for a compound using only the compound line the measured concentration of the compound may be unreliable particularly if other clusters are nearby the identity can still be considered accurate if the cluster shapes are clearly 10 4 Targeted Profiling 117 ENOMX CHENOMX NMR SUITE USER MANUAL discernible Using the compound line on tall isolated clusters generally provides accurate identity and quantity Tyrosine 19 um Aromatic region 0 02 M A wv au yet on NA Me E tagna oy A P Veg Synalar Spine Ps s Pme nN enti e Ps Sq Maye 0 00 0 02 Figure 10 1 Apart from these clusters in the aromatic region none of the other peaks for tyrosine are clearly visible Altho
249. uding concentrations transforms custom colors pins and stars Also compounds that appear in the Profiled Compounds set in the Compound Sets view Module in Chenomx NMR Suite that lets you analyze spectra by comparison with compound signatures from your Library creating a profile of the spectrum Used to mediate communication between a computer on one network and computers on other networks Sometimes used to improve network operations by caching frequently accessed data or to improve network security by acting as a secured gateway through which other computers access other networks like the Internet See PostScript Specific series of radiofrequency bursts and pauses in an NMR experiment designed to excite nuclei in a particular way before beginning to detect the resulting magnetization signal during the acquisition time Filter for the current view of the Compound Table based on entered text Displayed results can match to any or all of compound name compound comment compound ID or location in the spectrum in ppm Compound sets containing all Chenomx Reference Compounds currently appearing in your library The Reference Compound Sets are created and removed automatically by Chenomx NMR Suite as you add or remove Chenomx Reference Compounds from your library 149 evomx CHENOMX NMR SUITE USER MANUAL reference deconvolution Reference Panel relaxation delay residual binning reverse spectrum RGB
250. ugh it is clear that tyrosine is present the quantity of 19 uM should be considered approximate Subtraction Line For complex regions shapes use the subtraction line to determine an optimal fit for the cluster where possible Adjust the cluster height and position to remove the influence of the adjusted cluster while approximating a normal spectrum with the subtraction line Using the subtraction line is an advanced technique offering some of the most accurate shapes available but requires more time than other simpler techniques 0 02 Fumarate 19 um Overfit top Underfit bottom 0 02 0 01 j 0 02 0 00 0 01 0 00 Figure 10 2 The overfit subtraction line top center shows a negative residual peak and results in a concentration of 25 uM The underfit subtraction line bottom center leaves a positive residual peak and results in a concentration of 12 pM The accurate profile far right results in a subtraction line that approximates a smooth baseline through the area indicating that the signal has been effectively subtracted from the spectrum 10 4 Targeted Profiling 118 CHENOMX NMR SUITE USER MANUAL Fumarate 19 um Upfield top Downfield bottom 0 02 0 02 0 01 j 0 02 Figure 10 3 Inaccurate positions result in a combination of over and underfits A negative residual peak on the right suggests the cluster should be moved left or d
251. uick Search box shows a detailed status message You can also see the detailed status message in the tooltip that appers when you hover the mouse cursor over the status icon e When you hover the mouse cursor over some parts of the Compound Table tooltips appear containing more details For example hovering over the optional matched clusters column for a compound shows you which clusters are matched e You can set compound concentrations directly in the Compound Table by double clicking on a compound s concentration column and typing in a value e You can perform many common compound operations through the context menu available by right clicking on a compound s row in the table Operations accessible through the context menu include setting the compound to its maximum concentration automatically fitting it to the spectrum and clearing concentrations transforms custom colors stars and pins e You can copy the contents of a cell to the Clipboard by right clicking on the cell and selecting Copy cell name to Clipboard You can then paste the contents as text to any other program e Compounds that you have modified from their default state including concentrations transforms custom colors pins and stars will appear in the Profiled Compounds set and appear in bold in the Compound Table Press Delete with a a compound selected in the Compound Table to clear all concentrations transforms custom colors pins and stars for the sele
252. um overlays DE rri Spectrum 1 Click Remove All Spectrum Overlays Clear Spectrum Overlay in Spin Simulator enu Location d Tools gt Clear Spectrum Overlay and Compound Builder Icon s m Tips and Tricks e You can also remove all spectrum overlays by clicking on the red X beside the Overlay Lines section in the Legend e Youcanonly overlay spectra in the Chenomx NMR Suite format cnx Ifthe spectrum you would like to use is in a different supported format you need to import and save it in Processor before using it as an overlay e n Compound Builder and Spin Simulator you can only have one spectrum overlay at a time In Profiler and Processor you can have up to fifty spectrum overlays e In Compound Builder if you overlay a spectrum whose frequency does not match the magnet frequency specified in the Compound Details you are notified ofthe mismatch and given the chance to update the Compound Details to match the spectrum overlay Related Topics e Sidebar on page 16 e Chapter 5 Processor on page 28 e Compound Details on page 91 4 9 Spectrum Overlays 19 CHENOMX NMR SUITE USER MANUAL 4 10 Spectrum View Tools The Spectrum View contains the spectrum as a graph of intensity vs frequency In addition to the simple zoom and scroll that you may be familiar with in other software Chenomx NMR Suite includes a number of specialized tools for manipulating the Spectrum View Show Entire Spectrum Me
253. uring acquisition It may not be appropriate for all spectra Applying Reference Deconvolution 19 20 21 22 23 24 Switch to Reference Deconvolution mode Leave the Target Linewidth at its initial value of around 0 6 Hz If you also want to apply line broadening to the spectrum you may add the desired amount of line broadening to the target linewidth here For example to add 0 5 Hz of line broadening you would change the target linewidth here to 1 1 Hz Select the Use DSS TSP Satellites check box This option includes the 7 Si satellite peaks on either side of the DSS methyl peak in the reference deconvolution model Click the Accept button to apply your changes to the spectrum Switch to the CSI Editor The CSI definition needs adjustment following reference deconvolution as peak shapes have changed throughout the spectrum Itis good practice to double check the fit of the CSI peak any time you change the processing of a spectrum Click the Find Automatically button Applying Line Broadening 25 26 27 28 29 Switch to Line Broadening mode Enter a value of 0 4 Hz When you analyze spectra using the Chenomx library the ideal CSI linewidth is somewhere around 1 0 to 1 5 Hz to match the spectra originally used to create the compound signatures Since the spectrum started with a linewidth of 0 6 Hz adding 0 4 Hz here brings the spectrum into the ideal range You could also have added this value
254. utorials in this chapter can help you use any ofthe available modules more effectively 10 1 File Location Note You can find all files mentioned in these tutorials in the Samplesw folder in your Chenomx NMR Suite install folder 10 2 Processor Introduction You can use the Processor module to process your spectra in preparation for using them in Profiler Spin Simulator or Compound Builder Before processing your spectra add spectrum metadata The most important metadata to add is a CSI definition Processor adds some spectrum metadata based on the CSI type and concentration that you specify in the Import NMR Data dialog when you import the spectrum However Profiler Spin Simulator and Compound Builder use the CSI to determine lineshapes for any fit or simulation that you do so it is very important to define the CSI shape properly Once you have added spectrum metadata you can begin processing spectra There are a variety of processing effects available and itis possible to apply them in any order that you prefer However for the best results in any module we recommend the following processing order 1 Phasing Unless you need to reverse the spectrum phasing should always be your first processing step 2 Baseline Correction 2 point linear or cubic splines Even if your spectrum appears to have a fairly flat baseline consider applying a simple baseline correction layer to ensure that the spectrum baseline aligns with that
255. ve seen about 13 Hz 28 Adda J modifier to SD1 and couple it to SDO using a J value of 13 Hz Since the signals for SDO and SD1 in the spectrum both appear simpler than you might expect given that they are coupled to five other signals it seems reasonable that the remaining two coupling constants for each spin definition will be similar The uncoupled splits that are available are associated with SD4 7 44 Hz and 6 88 Hz and SD5 7 40 Hz and 6 67 Hz Thus the two larger coupling constants must be associated with SDO and the two smaller with SD1 or vice versa A quick test of each alternative indicates that the former option yields a better approximation of the spectrum 29 Adda modifier to SD1 and couple it to SD4 using the smaller of the available uncoupled splits 6 88 Hz 30 Adda J modifier to SD1 and couple it to SD5 using the smaller of the available uncoupled splits 6 67 Hz 31 Adda J modifier to SDO and couple it to SD4 using the remaining uncoupled split 7 44 Hz 32 Adda modifier to SDO and couple it to SD5 using the remaining uncoupled split 7 40 Hz 33 UsetheJ Value Editor to fine tunethe modifier coupling SDO to SD1 The resulting value is 13 23 Hz 34 Adjust the frequency height and width of SD1 and SDO to better fit the spectrum 35 Savethesimulation file If you would like to review the sample simulation of proline do not replace the file called Samples Spin Simulator NMProline xss 10 6
256. w do edit a Smart Compound Set 1 Selecta Smart Compound Set in the Compound Sets view 2 Click Edit Smart Compound Set 3 Make any desired changes to the name of the set magnet frequency restriction or filters 4 ClickOK 9 4 Compound Set Tools 102 CHENOMX NMR SUITE USER MANUAL Tips and Tricks e You cannot manually add compounds to a Smart Compound Set Only compounds in your library that match the filters that you define in the Smart Compound Set appear in the set Use Edit Smart Compound Set to modify the compounds appearing in a Smart Compound Set e When you change the contents of any compound set its name and icon in the Sidebar throbs for a couple seconds to indicate which set has changed If you have made a change that affects multiple compound sets all of the affected sets will throb e Smart Compound Sets update automatically as the contents of your library change When you add a new compound to your library it appears in any Smart Compound Set whose filters it matches even if you created the Smart Compound Set before you added the new compound e Editing the filters of a Smart Compound Set is the only way that you can modify the contents of a Smart Compound Set You cannot directly add compounds to or delete compounds from a Smart Compound Set Related Topics e Library Tools on page 96 e Compound Sets Sidebar on page 100 e Compound Sets on page 101 e Rename Compound Sets on page 103
257. water signal When you profile compounds with multiple clusters use clusters well away from the water signal to determine compound quantities This may result in a slight overfit sum line higher than spectrum line of the clusters closer to water but gives you more consistent and accurate concentrations Lactate 1719 um rio bio Cluster 1 suppressed Cluster 0 Hos Fo s Los bos pos foe slightly overfit N poe Fo oN J al gt gt n us t Figure 10 7 Since cluster 0 right is quite far from the water peak it experiences little suppression Profiling lactate based on cluster 0 results in a slight but acceptable overfit of cluster 1 left 10 4 Targeted Profiling 120 ENOMX CHENOMX NMR SUITE USER MANUAL Lactate 1719 um po bio Cluster 1 suppressed Cluster 0 Calc 1531 uM 10 9 gt r T A m 4 10 135 1 30 Figure 10 8 Profiling lactate based on cluster 1 left incorrectly reduces the reported concentration by almost 1196 Best Guess When you profile a compound with multiple clusters you may encounter a cluster that is difficult to profile accurately due to a lack of prominent peaks in the signature or in the spectrum or both In this case use minor adjustments to approximately match the sum line to the spectrum line the goal here is mostly aesthetic since very little information is available to produce an accurate profile If all of the clusters for a compound mu
258. yruvate since it has the highest Maximum Concentration Use Fit Automatically to suggest a concentration and transforms for pyruvate press the space bar Adjust the pyruvate signature blue as needed to match it to the corresponding peak in the spectrum black Clear the quick search box Click Show Entire Spectrum Water Suppression Effects Profiling Alanine 17 18 19 20 21 22 23 24 Zoom in on the doublet near 1 50 ppm Right click on the doublet and click Filter for Compounds Near 1 47 ppm In the Compound Table select alanine Use Fit Automatically to suggest a concentration and transforms for alanine press the space bar Adjustthe height ofthe alanine doublet blue as needed to match the corresponding doublet in the spectrum black You should not normally increase the height of a signature above the black line so use the right most peak to determine the appropriate height Move to the second cluster of alanine 3 8 ppm using the Cluster Navigator and adjust its frequency as needed to match the spectrum Since the second cluster is much closer to water than the first one itis more sensitive to side effects of the water suppression pulse used to acquire the spectrum Thus the cluster at 1 5 ppm is a good choice for determining the concentration of alanine while the cluster at 3 8 ppm must be fit using only frequency adjustments For more details on handling water suppression effects

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