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1. 1 30 Figure 11 8 Fitting lactate based on cluster 1 left incorrectly reduces the reported concentration by almost 1196 Best Guess When you fita compound with multiple clusters you may encounter a cluster that is difficult to fit 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 fit the sum line to the spectrum line the goal here is mostly aesthetic since very little information is available to guide an accurate fit If all of the clusters for a compound must be fit using this technique the fit of the compound both identity and quantity should be considered unreliable 11 4 Tutorial Targeted Profiling 113 CHENOMX NMR SUITE USER MANUAL ENOMX 0 06 O Phosphocholine 35 uv Clusters 3 and 4 0 04 I 0 02 a S 0 00 0 06 0 04 I 0 02 m M 0 00 T T T T T 4 26 4 24 422 420 4 18 4 16 4 14 442 Figure 11 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 fitting some compounds you may find that a cluster is not visible in the signature or thespectrum or both at concentrations consistent wit
2. 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 29 for details Tips and Tricks e Successfully applying reference deconvolution to your spectrum requires good phasing and baseline correction You should not apply reference deconvolution to a spectrum that is poorly phased or has a poor baseline e The target linewidth text box initially contains the native linewidth of your spectrum based on your CSI definition 6 4 Processing Tools 37 evomx A Processing gt Advanced gt Water Menu Location Deletion Icon s WD Ctri Alt 5 Hotkey s Cmd Alt 5 CHENOMX NMR SUITE USER MANUAL e Choosing a 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 Related Topics Importing Spectra on page 16 e Processing History on page 32 e Phasing on page 34 e Baseline Correction on page 35 e Line Broadening on page 36 e Convert Spectra on page 39 Water Deletion In many spectra of biofluids or cell extracts the water peak may be very large In
3. 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 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 You should use these clusters only when no alternative is available and recognize that concentrations based solely on these clusters may be unreliable Table 11 1 Expected Concentrations for Basic Start cnx Compound Conc mM Compound Conc mM 3 Indoxylsulfate 0 3692 Formate 0 2474 4 Hydroxy 3 methoxymandelate 0 0425 Fumarate 0 1236 Acetate 0 4899 Niacinamide 0 4641 Alanine 0 5208 Pantothenate 0 0791 Citrate 0 4007 Pyruvate 0 4789 DSS Chemical Shape Indicator 0 4830 Urea 147 1484 Part Il 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 fitting a com
4. simplified molecular input line entry specification simulation details simulation file simulation line smart compound set SMILES spectral binning spectral width spectrum details spectrum file spectrum line spectrum overlay spectrum overlay line spectrum thumbnail 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 if the spectrum is then saved from Profiler and closed See standardized intensity 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 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 defined including coupled and uncoupled splits Chenomx file format xss designed to store the parameters of simulations created with Spin Simulator Lineinthe 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
5. 16 39 JCAMP DX spectrum file jdx 16 JEOL Delta spectrum file jdf 16 line 23 NMRPipe spectrum file fid 16 overlay 19 pH 30 remove overlaid 19 reverse 39 thumbnail 22 Varian spectrum file fid 16 Spectrum View 20 21 53 68 82 spin definition 67 navigator 68 system 66 67 spin definition add 67 edit 67 panel 66 69 remove 67 spin system add 66 remove 66 split count 6 69 splitting factor 6 star 44 47 statistical analysis 56 58 export profiled concentrations 56 spectral binning 58 subtraction line 23 110 fit 110 sum line 23 111 fit 111 supported file types Bruker processed data 1r 16 Bruker spectrum file fid 16 JCAMP DX spectrum file jdx 16 JEOL Delta spectrum file jdf 16 NMRPipe processed data ft2 16 NMRPipe spectrum file fid 16 Varian processed data phasefile 9 16 Varian spectrum file fid 16 svfph macro 9 T tape measure 22 target linewidth 37 temperature 9 time domain size 33 total area 29 58 transform 50 clear 50 window 50 81 transform window clear 81 default 81 edit 81 transposed layout 56 tutorial compounds proline 117 124 126 valine 115 121 126 U uncoupled split 6 69 undo zoom 21 ungroup uncoupled splits 69 update compound versions 96 profiled versions 54 update profiled versions all compounds 54 144 CHENOMX NMR SUITE USER MANUAL selected compound 54 starred comp
6. 5 3 Funda H 17 5 A Closing a Eilez ete vanudaracea an e RERUM EE aie E E 18 5 5 Exiting Module iae iaaa aaa aa AAE 18 5 6 Undo and Redo eerte iss denne ras ERR UAR ee ERR Eo UE ER X EUR OUS E A E Er op d 19 5 7 Change Colm Svs uii renani n AE enddul kane dcc c du Ng cue R ey 19 5 8 0yerlaying a Spectrum eii eter rte HE pet Eran posee a ie ioa rix EE 19 5 9 Spectrum View Tools ccc eis ct ie dna erue taa exi nx aiie anaE Eein AA EEES 20 Show Entire Spectrum iiit etre tA RERRE hee Ete REI UNE se v MERE EE 20 SOU ZOOM 20 Undo7 Red6o ZOOM 5 rp t petere n steer eae eee 21 evomx CHENOMX NMR SUITE USER MANUAL LuunPAvoum 21 Increase Decrease Vertical Zoom sese 21 Sende 21 Spectrum Thunibnail ete ip a EE AA eE 22 Select REGION enne cssnoqesc c eian ea a e e AAE E A A Raai 22 Tape Measures ereenn eneen a Ear dee Le a EEEN E E AEE 22 5 10 Display OPtiONS ERE 23 5 11 Preferences moriron enina E E EEEE 24 6 PrOCESSOT 27 AMO Jau rn 27 6 2 Quick Reference Guide eeeesssseeseeeeeeeee nennen nennen nennen ne nnne nnn nnn 28 6 3 Information Tools 5 1 etie ri En RE Eo Ruhr Le ER tae eu Fu r lvnE Era IEEE Cx ub e Ed 29 ja 29 PH Editor ricrea ETT 30
7. 6 5 Importing and Exporting Data 40 Chapter 7 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 7 1 Overview The following illustration shows the default Profiler display after analyzing a sample In this example the sum line of the Chenomx NMR Suite analysis appears in red and the original spectrum appears in black B Profiler Advanced End cnx A Sac File Edit View Compound Tools Help 88 a 00 OB Z _ Dy Profiled Compounds Serine J Serine E fy Chenomx 400MHz pH 4 9 40 39 El E By Chenomx 400MHz pH 6 8 E By Chenomx SoomHz pH 4 9 E y Chenomx Soom pH 6 8 E Chenomx 600MHz pH 4 9 V f Chenomx 600MHz pH 6 8 E By Chenomx 700MHz pH 4 9 E chenomx 700MHz pH 6 8 By Chenomx 800MHz pH 4 9 E fy chenomx s00MHz pH 6 8 Chemical Structure t Molecular Formula C3H7NO3 Molecular Weight 105 0926 gimol IUPAC Hame lt A m L Serine Alternate Names CAS Registry 0 0 56 454 Alternate CAS Registry External Database References KEGG Ligand Compound d ChEBI i PubChem Compound P eMolecules SMILES Search HMDB MetaboCard amp Compound Na
8. Green Glycolate Glycolate 691 pM 1 9 Purple Pantothenate Pantothenate 82 uM 21 1 T T T T T T 4 00 395 3 90 4 00 3 95 3 90 Figure 11 6 Considering all the compounds together along with confirmation using other clusters of serine and pantothenate gives a better fit 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 water signal When you fit compounds with multiple clusters use clusters well away from the water signal to determine compound quantities This may resultin a slight overfit sum line higher than spectrum line of the clusters closer to water but gives you more consistent and accurate concentrations 11 4 Tutorial Targeted Profiling 112 ENOMX CHENOMX NMR SUITE USER MANUAL Lactate 1719 um Cluster 1 suppressed slightly overfit Cluster 0 gt rA 4 10 Figure 11 7 Since cluster 0 right is quite far from the water peak it experiences little suppression Fitting lactate based on cluster 0 results in a slight but acceptable overfit of cluster 1 left Lactate 1719 uv Cluster 1 suppressed Calc 1531 uM 10 9 RI Cluster 0 m 1 30
9. The Spin Navigator allows you to quickly move among the spin definitions that you have created in the current simulation It appears in the top left corner of the Spectrum View as a ordered list of the approximate positions of all the spin definitions of the simulation in ppm When 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 Menu Location Hotkey s View Show Spin Navigator Ctrl Shift N Cmd Shift N 1 Make sure that the Spin Navigator is visible 2 Click a 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 8 3 Fitting Tools 68 CHENOMX NMR SUITE USER MANUAL 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 66 e Spin Definitions on page 67 e Spin Definition Tab on page 69 e Simulation Details on page 71 Spin Definition Tab The Spin Definition Tabs found in the Spin
10. 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 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 Quick Searches on page 89 e Send to Compound Builder on page 91 e Show Archived Compounds on page 91 e Remove Selected Compounds from Library on page 92 e Rescan Compound Library on page 92 e Compound Set Tools on page 93 10 3 Library Tools 88 exomx CHENOMX NMR SUITE USER MANUAL Quick Searches The number of compounds appearing in the Compound Table can make it difficult to locate a particular compound Quick Searches allow you to 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 How do limit the compounds visible in the Compound Table Icon s Hotkey s RH Ctrl L Cmd L 1 Click the binoculars icon at the left edge of the search box t
11. ee cay Ern ret t tx Eee rr eno Ee RN SER haa vs bx o ERR E Ee ns 51 Scale ConcentratiOns cis ccidccctncssedsancndvecrysdscsieneticvesdecacdsanendvessecteotsanctddeens 52 Cluster Navigator eee be nemis H usu RR DA EEEa 53 TA Compound Set TOONS 22 cnet ataa E IER uPXRIDARIS DIMAQuA 53 Compound Set Panel rotto E ERN ERES EXER NEURERENM FER I E 53 Update Profiled Version One Compound eese 54 Update Profiled Versions Several Compounds esee 54 Open Library Mariager uiosieexescsesecsozesisxka dien eeiRub Ra el isa esr aaa iR 55 7 5 Importing and Exporting Data ssesseseseseee enne 56 Export Profiled Concentrations sseseeeenm een 56 Export Profiled Compounds sssssenmenenn 57 Im port Profile fee M 57 Spectral Binning epe MEC Retour EnePeu kd RE OEU EATEN eee 58 Export Spectrum Graphic tese deecticuk eras usbxu rte quk excessus ce ded gos 59 Copy Spectrum Image to Clipboard sseseeeenmm 60 Send to ProceSSOF iscccssstciascessaccaieed cdancnaecad sanetciestcnancedaved cdaccneacd ternseasecs 60 CHENOMX NMR SUITE USER MANUAL 7 6 Information Tools aisi eterni tnn paene eti end ea sna eas rece xd inondation 61 Reference Panel esteri E SUPER EE MERE HE 61 Spectrum Details eur unsstexee ciet ei eiu S du E D AEEA AREG 61 Concentration Units oerte ntn ai in REP ERR ENKR RR ERE EFEF
12. 3 trimethylsilylpropionate TSP or TMSP or formate may be used as a CSI However TSP and formate are not recommended as their chemical shifts are sensitive to pH If you choose not to add any pH indicators to your samples you need to supply a pH value measured to an accuracy of 0 01 for proper analysis with Chenomx NMR Suite 3 2 Spectral Data Acquisition For the best results from your analysis with Chenomx NMR Suite you must acquire high quality spectra You should pay particular attention to proper shimming phasing and baseline correction to produce spectra that you can accurately analyze and interpret using Chenomx NMR Suite Pulse Sequences Using Chenomx NMR Suite you can quantitatively analyze spectra produced by NOESY 100 ms tyi You can use other pulse sequences for identification purposes but quantification based on these pulse sequences may be unreliable 3 1 Sample Preparation 8 evomx CHENOMX NMR SUITE USER MANUAL Required NMR Parameters For the best results from Chenomx NMR Suite when analyzing your data you should 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 3 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 In o
13. Builder if you have purchased the Professional edition of Chenomx NMR Suite or if you are using a time limited trial version of Chenomx NMR Suite The Compound Builder module allows you to create compound library entries so that you can identify and quantify user defined compounds using Chenomx NMR Suite You can integrate the compound signatures that you create with Compound Builder into a user defined compound library using Library Manager 9 1 Overview ed amp Compound Builder Prolinexcpd Proline cnx c File Edit View Compound Tools Help P 6e in n IZ z mel wov iL amp Proline 3 Proline waa a aa El Chemical Structure o a 4 OH NH Molecular Formula CsHgNO Molecular Weight 115 1305 gimol IUPAC Hame L Proline Alternate Names CAS Registry 147 85 3 Alternate CAS Registry External Database References Clusters ppm Peaks ppm KEGG Ligand Compound c Selection 1 97824 ChEBI d 2 01137 Center ppm 2 33894 Width sw Various PubChem Compound P Amplitude si 0 32175 td eMolecules SMILES Search HMDB MetaboCard 2 Environment Overlay Magnet Frequency MHz 799 81 pH 6 93 Cluster Navigator Allows you to navigate among the clusters of the currently open compound You can enable or disable the Cluster Navigator using the View menu Spectrum View Displays the spectrum as
14. CHENOMX NMR SUITE USER MANUAL e Generate Cluster for Region on page 80 e Transform Windows on page 81 e Cluster Navigator on page 82 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 but the Information Panel always allows you to select either How do I select a cluster Menu Location Select by Cluster Ctrl B Hotkey s Cmd B 1 Turnon selection by cluster if it is not currently on 2 Clickonthecluster in the Spectrum View Alternately click on the cluster s position in the Information Panel How do I select a peak 1 Turn off selection by cluster if it is currently on 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 3 Click each of the peaks or clusters that you would like to select 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 h
15. For example analysis of an extended dataset may require profiling a fixed set of compounds 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 allow you to 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 Compound Sets that you have set to auto update will always update themselves to contain the latest version of each compound in the set Compound Sets that are not auto updating show you status indicators marking the compounds that have been updated or removed How do I create an empty new Compound Set 1 ClickNew Compound Set 2 Enteraname for the new Compound Set 3 Startadding compounds from your library or other Compound Sets How do create a new Compound Set containing specific compounds 1 Selecta 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 ClickAdd to
16. Grouping Peaks as a Cluster sesseseseseeem mmm 79 Optimize Selected Peak Shapes sseseseeeeeemn 79 Generate Cluster for Region sssseenem mene 80 Transform Wind OWS RE 81 Cluster Navigator eee eet kot Re eee E E E Seen Peg ER Res 82 94 Information Tools eine etn esee netos sn kno saei erede sa ne PLE Er ed asas 83 Reference Panel iier rr eta bred er ERROR EA ERE YT RS UO RE MEO UE 83 Compound Details rnnt coed ooxu dace a eR pxAl e IRA MP aii 84 Information Panel erit tx rre ert EXPE RE REIR a ra ER FE SegE ERE 85 10 Library Manager MEE ER 86 MIEEED Oau ls 86 10 2 Quick Reference Guide ceccecceeeeeeeee sence eeeeeeeeee esses esses nennen nennen 87 10 3 Library Tools eR rene SEE e Crate ea bosse ese eR Een erENS 88 Compound Table Dmm 88 Quick Searches uso stan ninien ein ET R O E EE EE EEA EAE ES 89 Import Compo unds retreat isst aa a DA e EAA E 89 Export as Compound Pack soirceas E A E ea 90 Send to Compound Builder sssssseeeeeeee ka 91 Show Archived Compounds c ccceeeeeee neta eee eee eee eeaeeeeeeeeeeaeeeaeeaae 91 Remove Selected Compounds from Library ccccceeeeeeeeeeeeeeeeeeeenees 92 Rescan Compound Library cirerer i ttt eoe RE EET HEN Eur eeu REPRE REA FEES 92 10 4 Compound Set Tools eode deni nacen eia eo ssa sepe dab x ada i x rr cR EE 93 Compound Set Panel t re bom E pc RE OR a
17. How do I remove a spin definition Menu Location Icon s Simulation gt Remove Spin Definition x 1 Selecta spin definition using the Spin Definition Tabs or the Spin Navigator 2 Click Remove Spin Definition Tips and Tricks Aspin 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 required e A spin system can contain 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 71 e Height adjustments always affects 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 e Removing a spin definition also removes any J modifiers that you have associated with that spin definition Related Topics e Spin Systems on page 66 e Spin Navigator on page 68 e Spin Definition Tab on page 69 e J Modifiers on page 69 e Simulation Details on page 71 Spin Navigator
18. If you want to create a compound for each valid pH range change the transform windows to match the range that you did not enter previously update the Compound Details to match the new range and save the compound file to a different filename Part Il Complex Compound Now that you have developed a basic familiarity with the tools available in Compound Builder you are ready to use them to create a compound signature for a more complex compound proline O 3 6 47 NZ Now 5 N 1 H Creating a Compound Signature for Proline 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 When prompted to calibrate the simulation environment 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 11 6 Tutorial Compound Builder 124 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
19. Redo Zoom y Zoom Auto Zoom Ctrl F Cmd F je Zoom Increase Vertical Zoom Zoom gt Decrease Vertical Zoom Edit Mode CSI m Edit Mode pH zem 5 E Show Processing History Ctrl Shift H Cmd Shift H Show Spectrum Line Ctrl Shift 1 Cmd Shift 1 6 2 Quick Reference Guide 28 e CHENOMX NMR SUITE USER MANUAL Ge ow Linux Windows MacOS X HI I Select Region Ctrl T Cmd T Processing Menu po Phasing Ctrl Alt 1 Cmd Alt 1 ace Baseline Correction Ctrl Alt 2 Cmd Alt 2 tae Line Broadening Ctrl Alt 3 Cmd Alt 3 aD Advanced gt Reference Deconvolution Ctrl Alt 4 Cmd Alt 4 we Advanced gt Water Deletion Ctrl Alt 5 Cmd Alt 5 as Advanced Reverse Spectrum Ctrl Alt 6 Cmd Alt 6 Tools Menu J Find CSI Automatically x Find pH Automatically a ia Convert Spectra Help Menu 2 Contents F1 F1 2 Search oe P Ld Save Application Log non A E Activation Details 9 About Chenomx NMR Suite 6 3 Information Tools In addition to processing the spectrum itself you can add extra information to a spectrum that allows you to analyze the spectrum in Profiler or create compound signatures and simulations 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 i
20. Tips and Tricks e Potential concentrations in Profiler refer to estimates that are subject to error based on assumptions that may not coincide with your interpretation of the spectrum You should verify any results that you obtain based on potential concentrations e You can set all of the compounds in the Compound Table to their potential concentrations On the Compounds menu select Set to Potential Concentrations Related Topics e Compound Table on page 44 e Starred Compounds on page 47 e Quick Searches on page 48 e Concentrations on page 49 e Compound Set Tools on page 93 Scale Concentrations Scale Concentrations allows you to 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 systematic influences on compound concentrations How do I scale the concentrations of all compounds by a common factor Compounds All Compounds Menu Location d Scale Concentrations Icon s LHe 1 Onthe Compounds 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 Click OK How do scale the concentrations of starred compounds by a common factor Compounds gt Starred Menu
21. X Scale m m Y Scale lol Zoom Show Entire Spectrum Ctrl Cmd Zoom gt Set Zoom Ctrl M Cmd M Zoom Undo Zoom R Zoom gt Redo Zoom y Zoom Auto Zoom Ctrl F Cmd F je Zoom Increase Vertical Zoom 9 2 Quick Reference Guide 73 evomx CHENOMX NMR SUITE USER MANUAL 1 Zoom Decrease Vertical Zoom Linux Windows MacOS X Transform Window Edit for Selected V amp Show Reference Panel Ctrl Shift R Cmd Shift R Show Cluster Navigator Ctrl Shift N Cmd Shift N Show Overlay Line Ctrl Shift 1 Cmd Shift 1 Show Subtraction Line Ctrl Shift 2 Cmd Shift 2 Show Compound Line Ctrl Shift 3 Cmd Shift 3 Show Selection Line Ctrl Shift 4 Cmd Shift 4 Lu m Overlay Spectrum I e i Select Region Ctrl T Cmd T Compound Menu UU LS Add Peak Ctrl K Cmd K m Edit Selected Peaks Ctrl E Cmd E Ligh Remove Selected Peaks Delete Delete La Group Selected Peaks as Cluster Ctrl G Cmd G b rn 3 va amp Cluster Transform Window gt Set Default on Selected Clusters Transform Window gt Clear for Selected Clusters Transform Window gt Set Default on All Clusters Transform Window gt Clear for All Clusters Previous Cluster Ctrl Shift Comma Cmd Shift Comma Next Cluster Ctrl Shift Period Cmd Shift Period Tools Menu 8 Optimize Selected Peak Shapes Ctrl I Cmd I 8 Generate Cluster for Region Ctrl Shift I Cm
22. click Selected Compound gt Clear gt Highlight or clear the check box for the compound in the Highlighted column 7 3 Profiling Tools 46 Enom CHENOMX NMR SUITE USER MANUAL Tips and Tricks e Highlighting a compound adds it to the Profiled Compounds set even if you have not set concentrations or transforms for the compound e Highlight settings are stored with the spectrum when you save it as a cnx file The compound that you highlight remains highlighted when you next open the file until you clear the highlights Related Topics e Compound Table on page 44 e Custom Colors on page 46 e Starred Compounds on page 47 Starred Compounds Starring compounds allow you to mark them for future reference or to perform group operations on them including setting them to potential concentrations scaling concentrations and clearing concentrations transforms custom colors highlights 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 Menu Location Icon s Compounds Selected Compound Clear Star E 1 Selectthe compound in the Compound Table 2 Inthe Compounds menu click Selected Compound Clear Star or click the yellow star for the compound in the Starred
23. considered the number of virtual protons to which the spin definition would need to be coupled in order 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 methyl 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 acompound for which the Star column has been toggled 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 Concentrations and transforms for a compound are manipulated so that the subtraction line green approximates a normal 138 evomx CHENOMX NMR SUITE USER MANUAL sum line sum line fit svfph SVE SVgz Sw targeted binning targeted profiling text filter time domain size TMSP transform transform window tran
24. if your license has expired the Chenomx License Activation dialog appears Otherwise on the Help menu click Activation Details E mail the activation key listed in the dialog to Chenomx Technical Support at lt support chenomx com gt If you do not have access to e mail call Chenomx Technical Support at 1 780 432 0033 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 Technical Support 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 License Activation dialog appears again Click the Select 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 Proceed button to run the module that you selected You can view your activation details at any time by clicking Help Activation Details in any module Tips and Tricks 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 but each user will need to activate separately with the same license file New major releases for example version 4 x to 5 x require
25. is mcr Tools Menu Spectral Binning En Help Menu m Contents F1 F1 Search xe kd Save Application Log wae E Activation Details sss 9 About Chenomx NMR Suite 7 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 fit 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 fit to your spectrum as well as those that you have already fit along with their potential and profiled concentrations 7 3 Profiling Tools 44 evomx CHENOMX NMR SUITE USER MANUAL 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 The currently selected compound in the Compound Table is the active compound in the Spectrum View allowing you to manipulate its concentration and transforms You can filter the current contents of the Compound Table using Quick Searches This 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 the
26. jdx JEOL Delta spectrum data J modifier J value J value editor In Profiler the lines used to indicate highlighted compounds Colored to match the default selection line blue by default or the custom color for each compound if one has been assigned In Profiler a compound with a check in the Highlighted column of the Compound Table The signatures of highlighted compounds always appear in the Spectrum View regardless of what is selected in the Compound Table pH indicator supported by Chenomx NMR Suite Most accurate for pH 5 50 to 8 80 Refers to expanding the compound library by adding signatures from one or more compound sources including compound packs pack compound files xcpd andlegacy Chenomx NMR Suite files cnx and cnxlib 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 allows acomputer to run a Java application Chenomx NMR Suite is a Java application Spectrum data unprocessed or processed stored in the JCAMP DX data interchange format See JEOL Delta spectrum data See JCAMP DX spectrum data Data from spectra acquired using JEOL spectrometers and processed where applicable using the De
27. non overlapped peaks elsewhere in the spectrum see Cluster Navigator on page 53 a Ifthey are present i Fitthe non overlapped peaks to help establish a concentration range for the compound see Concentrations on page 49 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 50 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 50 4 4 Fitting Overlapped Regions in a Spectrum 14 evomx CHENOMX NMR SUITE USER MANUAL 3 Once you have approximately fit most of the groups in the overlap region fine tune the heights and frequencies of each cluster in the region to obtain an optimal fit You can use the subtraction line to guide your fit as a well fit cluster will leave a subtraction line that resembles a normal spectrum with the effects of the cluster removed 4 In overlap regions fit multi peak clusters before single peak clusters Also if urea is present you may want to fit it las
28. set the default transform window for all clusters Menu Location gt Set Default on All Clusters ey 1 OntheCompound menu select Transform Window gt Set Default on All Clusters Icon s 9 3 Fitting Tools 81 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 Menu Location View gt Show Cluster Navigator Ctrl Shift N Cmd Shift N Hotkey s CHENOMX NMR SUITE USER MANUAL How do I clear the transform window for a cluster 1 Selectthe cluster for which you would like to clear the transform window 2 OntheCompound menu select Transform Window 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 Atransform window applies to the center of a cluster and not the positions of its outermost peaks As a result you should consider only cluster centers when you decide on transform windows for your compounds e When you 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 You
29. 02 ppm 1 96 to 2 05 ppm 2 01 to 2 09 ppm 2 30 to 2 37 ppm 3 30 to 3 36 ppm 3 38 to 3 44 ppm 4 10 to 4 14 ppm 19 Ifyou entered a valid pH range of 4 00 to 9 00 in the Compound Details set the following transform windows a b c d f B Cluster at 1 978 ppm Cluster at 2 011 ppm Cluster at 2 058 ppm Cluster at 2 339 ppm Cluster at 3 328 ppm Cluster at 3 412 ppm Cluster at 4 121 ppm 1 92 to 2 04 ppm 1 93 to 2 07 ppm 2 00 to 2 12 ppm 2 27 to 2 39 ppm 3 25 to 3 39 ppm 3 36 to 3 48 ppm 4 05 to 4 18 ppm 20 Save the compound file If you would like to review the sample fit for proline you should not replace the file called Samples Compound Builder Proline xcpd 11 7 Tutorial Library Manager Introduction You can use the Library Manager module to add new compound to your library remove existing compounds and create and edit compound sets using the compounds in your library Sources of compounds that you can add to your library include 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 Importing Compounds To make use of compound signatures that you create using Compound Builder you need to add them to your library Importing compound files xcpd makes the compounds available in your library allowing you to
30. 14 Usethe frequency width and height controls to match SD5 as closely as possible to the spectrum line 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 17 Usethe frequency width and height controls to match SD4 as closely as possible to the spectrum line 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 0f 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 notappear quite large enough for a geminal coupling so use the latter to co
31. CHENOMX NMR SUITE USER MANUAL How do I remove an overlaid spectrum Menu Location Icon s Mew Salata Sena 1 Click Remove Overlaid Spectrum pectrum m Tips and Tricks e You can only 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 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 overlaid spectrum 5 9 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 Menu Location Icon s Hotkey s Show Entire Spectrum View Zoom Show Entire iion Show Entire Spectrum allows you to quickly expand the current view setting both the lol vertical 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 setting
32. ERE 62 8 Spin Simulator vse ccsavenss cazsneecaaneencnsteieesniantwncneatiancs SRI E SA B xEDA REP cIRI Eiai A 63 8 1 OVeEVIeW eco tenir re ERR abner ENXEA FER RS ue PIURM SAYS r EE E rR REEE ERE sand oni oe 63 8 2 Quick Reference Guide seeeesseeeeeeeee nennen nennen nennen nenne nenne nens 64 8 3 Fitting TOONS ges nd rt IM EUfeo UE I ERE EIE ME EU 66 IavejIEBDR HT 66 Spin Systems ccs aE ceps AEE Fk aD Een ERE EDM EM Cena REEF REFER coon ERA 66 Spin DeNMIIONS mm 67 Spin Navigator csivccsec sist cack cae tese Dd cdievtivegaadeieigasbbavctanwadecdanweinagiegoiaces 68 Spin Definition Tab p RS 69 J Modifieks 2 iere Deve ctn Rte x neck tack ee Keen ae EXE Eu theses EEEE 69 Simulation Details cm 71 9 Compound Builder eto anra aa tiie a x UMP I MI ME HP AER ERLUE 72 9 1 OVERVIEW 72 9 2 Quick Reference Guide ccccecceeeeee cece ee eeeeeeeeee enne nennen nennen nnns 73 9 3 Fitting TOOlS iiit iei h ten ete Rax eatis ba n sxesid inceddkeu gk E A AERE 75 New Compound cioe ut metuit ete ees een eM Le aue 75 port acm E 75 Add PO ak c raa e n e A E A 76 Selecting Peaks and CIUStEfS oaio ai A ENER 77 Remove Selected Peaks ii n t ttp tta tr tex RE npe nk ku E EXE eene 78 Adjusting Peaks oscccssuxt case eeccsieixk ona dot n XX ARP NeRUIEA RAE AURI dNIRIS REE 78
33. My Compound Setto 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 Set Panel How do remove compounds from a Compound Set 1 Selectthe Compound Set from which you would like to remove compounds in the Compound Set Panel 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 You must manually add compounds to a Compound Set Library Manager never automatically adds any compounds to a Compound Set 10 4 Compound Set Tools 94 evomx Menu Location Icon s Hotkey s File New Smart Compound Set p Ctrl Shift N Cmd Shift N 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 You can only remove compounds from Compound Sets and not Smart Compound Sets Related Topics e Library Tools on page 88 e Export as Compound Pack on page 90 e Compound Set Panel on page 93 e Smart Compound Sets on page 95 e Update Compound Versions on page 96 e Rename Compound Sets on page 97 e Delete Compound Sets on page 97 Smart Compound Sets In Library Manager you can create Compound Sets based on sets of rules that select compounds from yo
34. Processing HiStOLy oieseeeeseiexersiese ynasin kiedi n pania neidin nanakia a 32 Spectrum Details mrenani S SA DI RURAL M LHNIUE 33 6 4 Processing Tools 2 eit aaa une ku sux iiba dorsi iaeiiai 34 jiu Em 34 Baseline Correction P 35 Line Broadening oM A E 36 Reference DeconvolutiOTn siceciicsscsccdiacicecsccsssnseiaceesnddtannectsstondeceteunecdactinns 37 Water Deletion eiie iieri iret E ien eneee boe E xv e eun ER EE d lee Ese a Eii 38 Reverse Spectrum i i cese eesssene cesse eese toe dg ux Esa x epe E EASAN arua SAES AKESA 39 6 5 Importing and Exporting Data ssesseseeseeem mmm 39 Convert Spectra aieiecsesssesessxucss uet esssescexsexexk ocu s ER EXE aieiaa e eek AME isana 39 Send to Profiler ee ctr ere REIR REFER couse EEEE FI FL ru Ea 40 41 y o Oau sem 41 7 2 Quick Reference Guide seen nennen nennen nennen nenne nenne nn 42 7 3 Profiling Tools otro Er teles rete EIE tek Roto EE oro E ee 44 Compound Tables EE 44 Custom Colors eec Rete SURE che come ung tawkesuad ER SEX FEES MEOS WIS ERR MER ER 46 Highlighted Compounds sssssssseenm meme 46 Starred Compounds ue DEP e RUPEE RR rA eee EEE 47 Oiek SeaECli68 recon cied ac ateattugansuatensncud iunstcdetuaaceus e rec UE EEA 48 Concentrations iecore nonet hee r EUH ERU aee Le ree E Ebr RE PE s a ER UN E UR Ee REA 49 Jbconseintbee EU 50 Potential Concentrations
35. Spectra on page 39 6 4 Processing Tools 38 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 eene 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 to have Processor reverse the spectrum automatically Otherwise you can reverse the spectrum manually after you have imported it 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 Reverse Spectrum should be the first layer in your Processing History as other processing layers may be difficult to apply correctly with the spectrum backwards Related Topics e Importing Spectra on page 16 e Processing History on page 32 e Convert Spectra on page 39 6 5 Importing
36. 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 e 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 7 3 Profiling Tools 49 evomx CHENOMX NMR SUITE USER MANUAL 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 e To clear all of the concentrations for the current spectrum select Compounds gt All Compounds gt Clear Concentrations e To clear concentrations only for starred compounds select Compounds gt Starred Compounds Clear Concentrations All compound concentrations start out as unknown e 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 e When you Export Profiled Concentrations compounds with unknown concentrations are not exported unless other spectra in the exported set have those compounds profiled Related Topics e Spectrum View Tools on page 20 e Compound Table on page 44 e Starred Compounds on page 47 e Quick Searches on page 48 e Transforms
37. accuracy of fits that you may perform in Profiler Compound Builder or Spin Simulator based on the spectrum The pH editor allows you to calculate or set the pH for the current spectrum 6 3 Information Tools 30 evomx Menu Location View gt Edit Mode gt pH Menu Location Icon s Tools gt Find pH Automatically Xy CHENOMX NMR SUITE USER MANUAL If your sample contains any combination of creatinine imidazole or DFTMP you may be able to calculate the 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 For manual entry you should specify the pH to an accuracy of 0 01 Simin i 2 H pKa lo e p p 810 Be gu Figure 6 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
38. 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 11 5 Tutorial Spin Simulator 117 CHENOMX NMR SUITE USER MANUAL as well as coupling individually to the adjacent protons While this does mean that splitting patterns will be based exclusively on doublets n 1 it also means that there will be a lot more coupling interactions to keep track of Simulating Proline 1 Assign the spectrum matching protons in the structure of the compound with signals in the spectrum Note that this is often one of the largest tasks in fitting a new compound For proline the assignments are as follows protons labelled a project above the plane of the 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 b 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 c The signal for proton 3b appears at 2 058 ppm and couples to protons 2 3a 4a and 4b Spin Definition 2 or SD2 d The signal for proton 3a appears at 2 339 ppm and couples to protons 2 3b 4a and 4b Spin Definition 3 or SD3 e Thesignalfor proton 5a appears at 3 328 ppm and couples to protons 4a 4b and 5b Spin Definition 4 or SD4 f The signal for proton 5b appe
39. and Exporting Data Processor can help you to efficiently import raw 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 convert a group of spectra Menu Location Tools Convert Spectra 1 Start the Convert Spectra wizard zl s 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 9 3 Ifthe source spectra include multiple file 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 6 5 Importing and Exporting Data 39 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 16 e Storing the converted spec
40. changes 5 Click OK How do I couple two spin definitions using splits that have already defined 1 Selectone ofthe two spin definitions that you would like to link and select the uncoupled split that will link it to the other spin definition 2 Openthe Edit 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 remove a J modifier 1 Selecta spin definition 2 Selecta J modifier that you would like to remove 3 Click Remove J Modifier How do uncouple a J modifier 1 Selecta spin definition 2 Selecta J modifier that you would like to uncouple 3 Click Uncouple 8 3 Fitting Tools 70 Enom Compound gt Ungroup ad Uncoupled Splits 21 Icon s J Compound Group Uncoupled Menu Location n Splits Icon s J CHENOMX NMR SUITE USER MANUAL How do I ungroup uncoupled J modifiers 1 Selecta spin definition 2 Select an uncoupled split with a split count greater than 1 3 ClickUngroup Uncoupled Splits How do I group several uncoupled 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 Uncoupled Splits Tips and Tricks e J Modifiers can only link two spin definitions that are i
41. compounds rather than updating entire libraries when only a couple compounds may have changed 2 11 J Modifiers The concept of J coupling as it appeared in Signature Builder has been replaced in Spin Simulator by J modifiers which come in two varieties coupled and uncoupled Uncoupled J modifiers or uncoupled splits affect only one spin definition splitting it as though it was coupled to another spin definition but without actually coupling it to anything Uncoupled splits allow you to start simulating a cluster in the spectrum without necessarily defining all of its coupling relationships first You should consider the uncoupled state of a J modifier to be a temporary one in most cases all uncoupled splits should be converted to coupled splits before the simulation is considered complete Coupled J modifiers or coupled splits are equivalent to J couplings in Signature Builder in that they connect two spin definitions through a common J value formerly J coupling value and split count formerly splitting factor see below for details The split count found in Spin Simulator is slightly different from the splitting factor in Signature Builder The splitting factor defined the number of peaks that would result from the split and was independent of the cluster that you were coupling to Split count on the other hand defines the number of protons causing the split which for a simple split with a split count of n will result in n 1 peaks
42. compounds whose molecular weight has been specified and the accuracy of such concentrations depends on the accuracy of the molecular weight provided To change the molecular weight associated with a compound open it in Compound Builder and edit the Compound Details Related Topics Profiling Tools on page 44 Open Library Manager on page 55 Export Profiled Concentrations on page 56 Compound Details on page 84 Send to Compound Builder on page 91 7 6 Information Tools 62 Chapter 8 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 You should also know how to interpret NMR spectra especially J coupling Fitting complex compounds requires at leastthis basictheoretical 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 esque S
43. correction or reference deconvolution While importing a spectrum you may choose to have Processor automatically apply phasing adjustments Otherwise you can apply automatic or manual phase correction after you have imported the spectrum 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 1 Switch to Phasing mode 2 Automatic Click the Auto button to have Processor automatically calculate phase angles You should 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 3 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 4 Clickthe Accept button to apply your changes or click the Cancel button to discard them Tips and Tricks e Select one of the phase angle controls and use the arrow keys to make fine adjustments to the phase angle The arrow Keys allow increments of 1 in Normal mode 0 1 in Fine mode and 0 01 in Very Fine mode Proper phasing of your spectrum is essential to obtaining accurate analysis of your data with Chenomx NMR Suite 6 4 Processing Tools 34 CHENOMX NMR SUITE USER MANUAL e Aproperly phased spect
44. does not directly alter any fits you did with previous versions ofthe updated compound set When you load a spectrum in Profilerthat you fit with an earlier compound set the compounds with new versions available are marked in the Status column ofthe Compound Table You then have the option of updating them or retaining the original signatures Related Topics Update Profiled Version One Compound on page 54 Update Profiled Versions Several Compounds on page 54 Compound Sets on page 94 Smart Compound Sets on page 95 Rename Compound Sets You can rename both Compound Sets and Smart Compound Sets after you have created them How do I rename a Compound Set or Smart Compound Set Menu Location Icon s Hotkey s File Rename Compound Set 1 F Ctrl R Cmd R 2 3 4 Select a Compound Set or Smart Compound Set in the Compound Set Panel Click Rename Compound Set Enter a new name for the set Press Enter Tips and Tricks Right click on the name of a Compound Set or Smart Compound Set and select Rename to rename the set You can also rename a Compound Set or Smart Compound Set by clicking again on the name of a selected set in the Compound Set Panel You can rename a Smart Compound Set via the Edit Smart Compound Set dialog Related Topics Compound Set Panel on page 93 Compound Sets on page 94 Smart Compound Sets on page 95 Delete Compound Sets You can delete bo
45. e Chapter 9 Compound Builder on page 72 e Compound Table on page 88 e Quick Searches on page 89 e Compound Set Tools on page 93 Show Archived Compounds When you import a different version of a compound that already exists in your library you View Show Archived can archive the existing version Show Archived Compounds allows you to review a list of Compounds these archived compounds from which you can open the archived compounds in Compound Builder or remove them from your library permanently Menu Location Turning on Show Archived Compounds adds a Compound Set called Archived Compounds to the list on the far left ofthe Library Manager window Select the newly added Compound Set to display the Archived Compounds list 10 3 Library Tools 91 CHENOMX NMR SUITE USER MANUAL Tips and Tricks e You can use an archived compound to replace a current version Open the archived compound in Compound Builder and use Save As to save the xcpd file on top of itself in your Compounds folder specified in Library Manager Preferences making it the new latest version of that compound e Archived compounds can be added to Compound Sets when they are not automatically updating but not to Smart Compound Sets Related Topics e Compound Table on page 88 e Quick Searches on page 89 e Compound Set Tools on page 93 e Update Compound Versions on page 96 Remove Selected Compounds from Libra
46. have Processor attempt to determine the spectrum pH automatically Manual 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 ofthe imidazole creatinine and DFTMP peaks respectively move as you adjust the pH You can determine a coarse pH simply by adjusting these lines as close as possibleto the five actual peaks in your spectrum 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 ofthe spectrum In this case itis imidazole Zoominonthe two peaks for imidazole Click the Automatic Vertical Zoom button to ensure the best view of the two peaks 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 Clickthe Show Entire Spectrum button to restore a view of the whole spectrum Once you have finished adjusting your spectrum in Processor you can Movethe spectrum directly to Profiler for further analysis using the Jump to Profiler button Save the spectrum for later analysis in Profiler for creating a simulation in Spin Simulator or for creating a compound signature in C
47. heights of the peaks match the experimental spectrum particularly well 16 Select the cluster near 1 03 ppm optimize it and refine the fit as needed 17 Zoom tothe cluster near 2 3 ppm using the Cluster Navigator select it and optimize the fit 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 creating 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 contributions 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 These are excellent candidates for pruning as the two peaks could be replaced with one without any significant decrease in the quality of the fit 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
48. is most useful for isolated low intensity clusters If you fit all ofthe clusters for a compound using only basic fits the quantity 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 discernible Basic fits of tall isolated clusters generally give accurate identity and quantity Tyrosine 15 um Aromatic region 0 02 M IN 4 3 ww yay N A hon s MP eMe tay HP Prag dure t eget nos Pr Pn edem Pf PHA Naat 0 00 Figure 11 1 Apart from these clusters in the aromatic region none of the other peaks for tyrosine are clearly visible Although it is clear that tyrosine is present the quantity of 19 uM should be considered approximate Subtraction Line For more refined fits use the subtraction line to determine an optimal fit for the cluster where possible Adjust the cluster height and position to remove the influence ofthe adjusted cluster while approximating a normal spectrum with the subtraction line Thisis an advanced technique offering some of the most accurate fits available but requires more time than other simpler techniques 11 4 Tutorial Targeted Profiling 110 CHENOMX NMR SUITE USER MANUAL Fumarate 19 um Overfit top Underfit bottom 0 02 0 02 0 01 j 0 02 0 00 l 0 01 0 00 Figure 11 2 The overfit subtraction line top center shows a negative
49. least one ofthese pH indicators present in the sample to attempt automatic pH detection If the pH cannot be detected you are asked to supply a value manually after the spectrum is imported Specify a pH value manually Useful if your sample does not contain either 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 5 3 Saving a File Auto Baseline Correction Reverse Spectrum Bruker only 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 Splin
50. library Your library contains all ofthe compounds that you can fitto a spectrum including all magnet frequencies pH ranges pulse sequences and so on Compound Table The Compound Table in Library Manager serves a different purpose from the one in Profiler The most obvious difference is that concentrations potential 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 allows you to modify them When you first open Library Manager the Compound Table displays the most recent versions of all ofthe compounds in your library see Show Archived Compounds on page 91 for more information on viewing older versions of compounds 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 fourteen 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
51. of compounds that you sim lat r tutorial if you have would like to add to your library These simulations can be imported into Compound Builder purchased the Professional edition of Chenomx NMR Suite if i time limited done ipie MAC Ee It can be very helpful to have the molecular structure of the compound you are simulating trial version of Chenomx NMR Suite available for reference purposes to create compound signatures that you can then add to your library Part I Simple Simulation In order to become familiar with the various tools available in Spin Simulator as well as with the basic process involved in creating a simulation you will simulate a simple compound valine 1 CH O 4 H3C soy 2 A 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 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
52. p RAVA e 6 2 12 Automatic Cluster Generation esee memes 6 2 13 New pH Indicator ect iden tote bun en tavit eon Ol ta Fea et xS ERR nears 7 2 14 Universally Unique Identifiers UUID seeeeemmIH 7 3 Handling Samples and Spectra e Eoi c OR Ente cx eiae EU ie BP e E EEEE 8 33 Sample Preparation 2iieucctsecsgecsei expect eB axe a ins paru iia sMUeR i nsR ed ErGdE 8 Internal Standard Solution sesseeeee men 8 3 2 Spectral Data Acquisition ssssssssseeeeee eene nenne 8 Pulse Sequences zt ena ET di ae eM I PM AR IEEE EDU E eee 8 Required NMR Parameters ssssssessseseeeeeenmene nennen nennen nennen 9 3 3 Spectral Data Processing eror ERICH espe lox l e e aye E cpN EE IEEE ERES 9 Data Processed with Other Software seseeee em 9 4 Common Tasks iei terrier ER EIFE Ex ERAK ESI iv exe a REFS FErE E FARK USER Ea 11 4 1 Processing a Spectr m eei sese iesxeue eden uan sonundada resni enia iiia 11 4 2 Fitting a SDectrum cisnienie eiee ensi a Passe ka e Ia E EA E I ar ERE da 12 4 3 Identifying Compounds ssssessesesseenen meme emn nennen 12 4 4 Fitting Overlapped Regions in a Spectrum sesesee eene 14 4 5 Determining Compound Concentrations ssesseseeeeeen 15 5 TNE Basics EEUU 16 HBBERIanruEBU Lm 16 5 2 Importing Spectra ied Etui PER EHETU E ota E A Encre E EE UMEE re 16
53. panel After applying reference deconvolution or line broadening you should readjust the CSI parameters to take into account any newly introduced changes in lineshape If you are using DSS or TSP as a CSI you can usually readjust the CSI using the Find CSI Automatically button in the CSI Editor see CSI Editor on page 29 Determine the sample pH using imidazole creatinine or DFTMP see pH Editor on page 30 Calculating sample pH in Processor requires the presence of at least one pH indicator For sample pH above 6 imidazole provides the best results while creatinine works best for sample pH 5 and lower For sample pH between 5 and 6 or for more general pH determination you should have multiple indicators in your samples Please note that you should not normally need to add creatinine to urine samples as it is naturally present in urine If desired delete the water peak from the spectrum see Water Deletion on page 38 Water deletion is optional and may not be necessary or desirable for all samples Save the spectrum see Saving a File on page 17 or jump to Profiler see Chapter 7 Profiler on page 41 to continue with your analysis 4 1 Processing a Spectrum 11 Enom Show Selection Line must be o enabled in order to view individual compound signatures It is enabled by default CHENOMX NMR SUITE USER MANUAL 4 2 Fitting a Spectrum Fitting a spectrum using targeted profiling is a ver
54. profiled compounds Compounds gt All Compounds gt 1 Update Versions j Icon s D Menu Location Open the Update Versions dialog Ifno compounds need updating you cannot access the dialog 2 Review the information in the dialog and select the categories of compounds you would like to update 3 Click OK How do I update starred profiled compounds Compounds Starred 1 Menu Locatii pcc Compounds Update Versions Star at least one compound in the Compound Table Icon s D 2 Open the Update Profiled Versions dialog for starred compounds If no starred compounds need updating you cannot access the dialog 3 Review the information in the dialog and select the categories of compounds you would like to update You can update out of date compounds missing compounds or both 4 Click OK Tips and Tricks e To determine why a compound needs updating select it in the Compound Table A message appears in the space immediately above the Compound Table describing the status ofthe compound in greater detail Related Topics e Compound Table on page 44 e Starred Compounds on page 47 e Import Profile on page 57 e Chapter 9 Compound Builder on page 72 e Chapter 10 Library Manager on page 86 Open Library Manager While profiling a spectrum you may want to define a new Compound Set that contains a Menu Location File Open Library Manager smaller list of compounds or modify a
55. reactivation while minor releases for example version 4 5 to 4 6 do not 1 3 Setting the Compound Library Folder The defaultlocation ofthe compound library on your computer will vary depending on your operating system Windows XP Documents and Settings username My Documents Chenomx Compounds 1 3 Setting the Compound Library Folder 2 CHENOMX NMR SUITE USER MANUAL Windows Vista Users username Documents Chenomx Compounds Linux home username Chenomx Compounds If you prefer to have your compound library stored in a different folder you should change the compound library folder before you install your compound packs Changing your compound library folder will not move any compounds that you have already imported How do I specify the compound library folder 1 u e w N Open the Preferences module Switch to the Library Manager preferences Under Compound Library Folder click the Browse button Locate the desired folder Click Select to select the specified folder Related Topics Preferences on page 24 1 4 Importing the Chenomx Compound Packs Due to the variety of compound packs available Chenomx does not distribute compound packs as part of the Chenomx NMR Suite installer Your compound packs should be included on your installation CD in the Libraries folder if not you will receive the compound packs that you have licensed separately either on CD via e mail or via a web
56. 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 uM The accurate fit 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 0 02 Fumarate 19 um Upfield top Downfield bottom 0 02 0 01 I 0 01 0 00 VA 0 00 6 51 6 50 Figure 11 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 downfield 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 fit far right Overlapped Regions Sum Line You will encounter situations in which the cluster you need to fit overlaps one or more clusters from other compounds regions fitting this description are often called busy regions You often need to fit compounds that have overlapped clusters in groups ensuring that the combined fit 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 U
57. 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 You should 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 You should apply water deletion after any other processing layers including phasing baseline correction and reference deconvolution While importing a spectrum you may choose to have Processor apply water deletion automatically Otherwise you can apply water deletion manually after you have imported the spectrum 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 Ifyour spectrum needs to be reversed but has not yet been reversed water deletion may not work as intended If necessary you should reverse the spectrum before applying water deletion Related Topics Importing Spectra on page 16 e Processing History on page 32 e Reverse Spectrum on page 39 e Convert
58. spectrum or specific locations in the spectrum Using the Compound Table you can assign custom display colors to compounds highlight 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 twenty 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 have at least one Compound Set selected in the Compound Set Panel in order to see any compounds in the Compound Table 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 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 potential concentration updating the profiled version of the compound to the latest version in your library assigning a custom color and clearing concentrations transforms custom colors stars and highlights e Compounds that have been modified in some way from their d
59. statistical analysis Spectra are divided into pieces or bins and the integrated area in each bin is considered for further analysis 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 Can be used as overlays in Compound Builder and Spin Simulator 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 displayed in the Spectrum View in Spin Simulator and Compound Builder to guide the construction of accurate simulations and compound signatures Line in the Spectrum View in Compound Builder and Spin Simulator corresponding to the overlaid spectrum colored black by default Miniature version ofthe Spectrum View that can be used to quickly navigate or zoom to different regions of the spectrum regardless ofthe currently viewed region or zoom level 137 evomx CHENOMX NMR SUITE USER MANUAL Spectrum View spin definition Spin Navigator Spin Simulator spin system spline split count standa
60. that you create 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 InChI or SMILES codes for valine you can enter them here as well 7 Inthe Advanced tab enter the molecular weight of valine to three decimal places 117 146 Also enter a valid pH range of either 4 00 to 9 00 or 6 00 to 8 00 Enter noesy as the pulse sequence 8 Click OK 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 experiment
61. the CSI peak to match it with the spectrum line black 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 Tips and Tricks In order to adjust the CSI settings for your spectrum Processor must be in the CSI Edit Mode 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 using 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 You should usually 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 reference deconvolution you need to establish new CSI parameters to ensure accurate quantification and generally good fits Related Topics Importing Spectra on page 16 pH Editor on page 30 Spectrum Details on page 33 Processing Tools on page 34 pH Editor The position and shape of signals for a compound in aqueous solutions can be very sensitive to pH The accuracy ofthe pH that you set for a spectrum may have an impact on the quality and
62. the familiar n 1 rule of NMR spectroscopy For uncoupled splits the split count is a theoretical number that you must specify since the spin definition is not actually coupled to anything yet For coupled splits the split count for a J modifier on the current spin definition is the number of protons on the spin definition to which the J modifier is coupled 2 12 Automatic Cluster Generation Compound Builder can automatically generate a cluster that fits a specified region of an overlaid spectrum up to 100 peaks However signatures based on this automated cluster 2 8 Editing Compounds in Your Library 6 evomx CHENOMX NMR SUITE USER MANUAL fitting are only useful in profiling spectra with characteristics similar to the source spectrum on which they are based Similar in this case refers to spectra having the same magnet frequency MHz acquired using the same pulse sequence under the same experimental conditions and with similar peak widths Using automatically generated signatures to profile spectra that differ significantly from the source spectrum will yield results that are imprecise at best if not outright inaccurate or misleading 2 13 New pH Indicator In addition to imidazole and creatinine Processor now supports the use of difluoro trimethylsilyI methyl phosphonate DFTMP as a pH indicator DFTMP has a single peak in a tH spectrum appearing between 0 19 and 0 22 ppm 2 14 Universally Unique Identifiers UUI
63. the frequency control on the horizontal axis to better position the second cluster over the corresponding signal in the spectrum The frequency control allows you to restrict the movement of the cluster to only one direction Since the second cluster is closer to water than the first one itis more subject 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 horizontal adjustments 11 3 Tutorial Profiler 103 evomx CHENOMX NMR SUITE USER MANUAL For more details on handling water suppression effects see Water Suppression on page 112 28 Clear the quick search box above the Compound Table by clicking the red X 29 Click Show Entire Spectrum Profiling the Remaining Compounds 30 Using the techniques discussed above you should be able to profile the remaining nine compounds in the spectrum You can check your results for all ofthe 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 Some clusters are more reliable than others when determining concentrations of compounds that have multiple clusters You should use clusters meeting as many of the following criteria as possible to set the concentration for such compounds
64. use information and externallinks from the Reference Panel see Reference Panel on page 61 to help establish the presence of particular compounds in the samples that you are analyzing 4 3 Identifying Compounds Chenomx NMR Suite provides computer assisted methods to fit 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 To identify specific compounds 1 Selectatleast one Compound Set in the Compound Set Panel see Compound Set Panel on page 53 2 Locateacompound in the Compound Table that you believe is presentin the sample and select it see Compound Table on page 44 3 Use the Cluster Navigator located in the top left corner of the Spectrum View to navigate among the clusters for the displayed compound see Cluster Navigator on page 53 4 2 Fitting a Spectrum 12 evomx CHENOMX NMR SUITE USER MANUAL 8 Set a concentration for the compound so that you can see the clusters clearly see Concentrations on page 49 For each cluster compare the shape of the selection line blue and the spectrum line black and decide whether it is reasonable that the selection line could be contributing to the spectrum line in the displayed region If the fit appears reasonable proceed to determine appropriate heights and transforms for the clusters of the co
65. well as the sum line and the currently selected cluster s or peak s Cluster and Peak Lists Allow you to edit select or remove clusters or peaks in the currently open compound Also allows you to define new clusters based on the currently selected peaks or clusters Information Panel Displays information relating to the currently selected cluster s and peak s Spectrum View Tools These tools allow you to navigate the spectrum more easily 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 Spectrum Thumbnail Displays a thumbnail image of the Spectrum View The thumbnail can also be used to navigate the spectrum at various zoom settings 9 1 Overview 72 Enom CHENOMX NMR SUITE USER MANUAL 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 9 2 Quick Reference Guide Linux Windows Mac OS X File Menu P New Compound Ctrl N Cmd N Open Ctrl O Cmd O Open Recent e B Close Ctrl W Cmd W tH Save Ctrl S Cmd S Save As P Import aus Compound Details Preferences Exit is Edit Menu V Undo Ctrl Z Cmd Z Redo Ctrl Y Cmd Y Select All Clusters Ctrl A Cmd A Select by Cluster Ctrl B Cmd B View Menu
66. 007 Pyruvate 6 00 to 8 00 November 23 2007 Quinolinate 6 00 to 8 00 November 23 2007 Riboflavin 6 00 to 8 00 November 23 2007 Ribose 6 00 to 8 00 November 23 2007 S Adenosyhomocysteine 6 00 to 8 00 November 23 2007 Salicylate 6 00 to 8 00 November 23 2007 Salicylurate 6 00 to 8 00 November 23 2007 Sarcosine 6 00 to 8 00 6 00 to 8 00 e 6 00 to 8 00 2007 Succinate 6 00 to 8 00 2007 Succinylacetone 6 00 to 8 00 2007 Sucrose 6 00 to 8 00 2007 Tartrate 6 00 to 8 00 2007 Taurine Theophylline 6 00 to 8 00 6 00 to 8 00 2007 2007 Threonate 6 00 to 8 00 23 2007 Threonine 6 00 to 8 00 2007 Thymidine Thymine Thymol 6 00 to 8 00 6 00 to 8 00 6 00 to 8 00 2007 2007 November 23 2007 Tiglylglycine 6 00 to 8 00 November 23 2007 trans 4 Hydroxy L proline 6 00 to 8 00 November 23 2007 trans Aconitate Trigoneline 6 00 to 8 00 6 00 to 8 00 November 23 2007 November 23 2007 Trimethylamine 6 00 to 8 00 November 23 2007 Trimethylamine N oxide 6 00 to 8 00 November 23 2007 Tropate 6 00 to 8 00 November 23 2007 Compound Set Panel Allows you to 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
67. 2 3 3 Spectral Data Processing 10 Chapter 4 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 4 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 a File on page 16 and Importing Spectra on page 16 If necessary reverse the spectrum plot Reverse Spectrum flips the spectrum in the frequency domain This function is only necessary for some Bruker spectra Adjust the phasing see Phasing on page 34 Apply baseline correction see Baseline Correction on page 35 as needed Define the CSI parameters see CSI Editor on page 29 Apply reference deconvolution to correct lineshape distortions see Reference Deconvolution on page 37 or apply line broadening to improve the signal to noise ratio see Line Broadening on page 36 If you would like to apply line broadening in addition to reference deconvolution you should apply reference deconvolution first You can add line broadening as a separate effect or during reference deconvolution in the second case add the desired value in Hz to the target linewidth in the reference deconvolution
68. 2 Setthe desired pH using any one of the following methods e Click the Find Automatically button e On the Tools menu click Find pH Automatically e Click and drag the pH slider bar to set the determined frequencies of imidazole creatinine and DFTMP to the actual frequencies of the 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 6 3 Information Tools 31 evomx Menu Location Icon s Hotkey s View Show Processing History b Ctrl H Cmd Shift H CHENOMX NMR SUITE USER MANUAL e Type the desired numeric pH into the text entry box to the right of the slider bar Tips and Tricks e 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 allow more detailed adjustments over a smaller pH range e Ifyou have selected TSP or formate as the CSI then changing the pH alters the scale since the frequencies of the TSP and formate peaks are pH sensitive e Processor must be in the pH Edit Mode to adjust the pH for your spectrum e Youmustsave your spectrum to retain the changes that you have made to the spectrum pH Related Topics Importing Spectra on page 16 e CSI Editor on page 29 e Spectrum Details on page 33 Processing History Process
69. 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 match the spectrum using the height frequency and width controls This spin definition has a width of about 1 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 For now simply choose one ofthe spin definitions with which to fit the simulation height Save the simulation file If you would like to review the sample simulation of valine you should not replace the file called Samples Spin Simulator Valine xss Complex Simulation Now that you have developed a basic familiarity with some ofthe tools available in Spin Simulator you are ready to use them to simulate a more complex compound proline O d 6 44 No Son 5 N 1 H The spectrum of proline will be much more complex than the spectrum of valine The protons at each position couple to
70. 8 export compound pack pack 90 concentrations 29 profiled compounds 57 profiled concentrations 56 spectrum graphic 59 export concentrations default layout 56 transposed layout 56 export spectrum graphic image options 59 exported concentrations txt 29 F filter for compounds in selected region 48 for compounds near x xx ppm 48 find CSI automatically 29 find pH automatically 30 first order phase 34 folder compound library 2 24 default 24 frequency domain size 33 frowns 35 G generate cluster for region 80 group peaks as cluster 79 uncoupled splits 69 H highlight 44 46 l image file types compressed SVG svgz 59 encapsulated PostScript eps 59 portable document format pdf 59 portable network graphic png 59 PostScript ps 59 scalable vector graphic svg 59 imidazole 8 11 30 import compound album file cca 75 CHENOMX NMR SUITE USER MANUAL compounds to library 89 profile 57 simulation file xss 75 spectrum 16 import to library compound file xcpd 89 compound pack pack 89 old library file cnxlib 89 spectrum file cnx 89 ZIP compressed file zip 89 increase vertical zoom 21 information panel 77 78 internal standard 8 J J coupling 69 J modifier 6 69 add 69 coupled split 6 69 edit 69 group uncoupled 69 J value 6 69 J value editor 69 list 69 remove 69 split count 6 69 uncoupled split 6 69 ungr
71. Builder those changes are not automatically included in pre existing compound sets This means that you can use that compound set to analyze spectra throughout a long term project with consistent results independently of any library updates that you may need to make for other projects Update Compound Versions allows you to update the compound signatures in a particular compound set to match the most recent versions of those compounds in your library How do update compound versions in a compound set Menu Location Set 1 Icon s le 2 Ctrl E 3 Hotkey s Cmd E 4 e e e e e e e e MERI TOCHUO File Update Compound 1 Versions Icon s T 2 Ctrl U Hotkey s Cmd U Select the compound set that you would like to update in the Compound Set Panel Click File Update Compound Versions Tips and Tricks You can choose to have compound sets automatically update their contents to match the latest versions in your library by right clicking on a set in the Compound Set Panel and clicking Auto Update Compound Versions The icon used for the set in the 10 4 Compound Set Tools 96 Enom CHENOMX NMR SUITE USER MANUAL Compound Set Panel changes from the normal type to the auto updating type You cannot use Update Compound Versions on Smart Compound Sets i By definition these always update to contain the latest versions of compounds in your library Updating compound versions in Library Manager
72. Click Select to select the specified folder Tips and Tricks e You should avoid light line colors with a light or white background as they are difficult to see on the screen or in a printout The low and high values for the default zoom must be at least 1 ppm apart You can maintain multiple separate compound library folders and switch among them using the Library Manager preferences You should close any open files before switching to a different compound library folder If you plan to modify any of the Chenomx compounds you may find it helpful to maintain one compound library folder in which to experiment a play folder and one that you will use for serious analysis a work folder In this case copy your current compound library folder to another location and rename it to indicate that itis your play folder When you want to experiment with the provided signatures change your compound library folder to the play folder otherwise change it to the work folder Table 5 3 Preferences Overview General Preferences Internet Preferences Enable Zoom Animation Allows you to configure Chenomx NMR Suite to access the Internet through a proxy server if needed or to disable connecting to the Internet entirely Toggles the zooming animations used when you change zoom settings in the Spectrum View Graph Preferences Background Color Spectrum Line Color Overlay Line Color Sum Line Color Com
73. Compound Library 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 selected folder or always use the specified folder Sets the folder used by Library Manager to store the compound files xcpd that make up your library 5 11 Preferences 26 Chapter 6 Processor The Processor module allows basic processing and conversion of spectra into the Chenomx NMR Suite format cnx Currently Processor can import raw data in Varian fid Bruker fid JEOL jdf and NMRPipe fid formats and processed data in Varian phasefile Bruker 1r JEOL jd f NMRPipe ft2 and JCAMP DX jdx formats Regardless of the source format Processor saves spectra as spectrum files cnx 6 1 Overview Brocco sempe M T File Edit View Processing Tools Help VE ovis il 5i Processing History l Q m 1 Phasing 4 Pad 2 Baseline Correction T i 3 Reference Deconvolution IA ip 4 Line Broadening 5 Water Deletion o 3 4 Details T T A a 10 8 6 4 0 cesis dem Chemical Shape Indicator DSS cw Width Hz 1 021 Concentration mM 0 484 Height si 0 968 Center ppm 0 00000 E Preserve CSI Area e e Find Automatically Switch to pH Editor Y 1 Spectrum View Displays the spectrum as well as guidelines used during pH determinatio
74. D Compound signatures in your library are identified by a UUID while the compounds themselves that is the physical entities as opposed to the their signatures are identified by the Chenomx compound ID The use of UUIDs has a number of implications that may not necessarily be obvious when you are creating new compounds for your library Changing the name of a compound in Compound Builder and saving it over the old file does not create a new compound but a new version of the same compound with a new name To ensure that it appears as a new compound in your library simply save it as a new file in the compound library folder To save it over the old file but still have it appear as a new compound open Compound Details go to the Advanced tab select the manual UUID option and click Generate When you save the file with the new UUID it will appear as a new compound in your library Saving a compound as a new file creates a new UUID in the file so it will be treated as a different compound in your library but potentially with the same name Chenomx compound IDs are not required in compound signatures that you may create but adding them allows Chenomx NMR Suite to display accurate compound information in the Reference Panel 2 13 New pH Indicator 7 Chapter 3 Handling Samples and Spectra DSS is hygroscopic in the solid form For accurate concentrations from a Chenomx NMR Suite analysis you must determine the final DSS concen
75. Definition Panel allow you to view and edit the properties of a spin definition and create edit or remove J modifiers How do I edit spin definitions and J modifiers using the spin definition tab 1 Selecta spin definition by clicking it in the Spectrum View or by selecting its tab in the Spin Definition Panel 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 e Click Remove to remove the selected J modifier in the current spin definition Tips and Tricks 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 current spin system are visible at any given time e Thetabs for spin definitions that are coupled to the one that you are currently viewing appear highlighted in bold in the Spin Definition Panel Related Topics e Spin Systems on page 66 e Spin Definitions on page 67 J Modifiers When you create a new spin definition it appears as a single unsplit peak J modifiers allow you to split a spin definition into more complex shapes to better fit real spectra J modifiers can be uncoupled affecting only on
76. File Close 1 Click Close kan m 2 Ifyou have made changes to the file and they are not saved choose whether you Ctrl W would like to save the changes 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 5 5 Exiting a Module 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 Ifnecessary choose a location and filename for the file Tips and Tricks You cannot exit a module with a file open that has unsaved changes without having the option of saving the changes If there are no unsaved changes the module exits without any further interaction 5 4 Closing a File 18 CHENOMX NMR SUITE USER MANUAL 5 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 Hotkey s Cmd Z CmdY 1 Click Redo Tips and Tricks e Only the last 100 changes
77. Graphics svg or Compressed Scalable Vector Graphics svgz Ifyou need an image that others can view or print on multiple computers use Portable Document Format pdf e Ifyou are preparing images for professional typesetting or publication use PostScript ps or Encapsulated PostScript eps e Inthe png format larger sizes result in more visible detail In the other formats higher qualities result in more visible detail when printed at the same physical size e Intheimage options step choose Do not shade area under lines to ensure that none of the peak shading effects are retained in the exported image This can be useful if you are exporting an image of an area containing many clusters as shading can create avery heavy look Related Topics e Spectrum View Tools on page 20 Copy Spectrum Image to Clipboard You can use Copy Spectrum Image to Clipboard to quickly make an image of the current Edit Copy Spectrum Image to spectrum available to paste directly into another application without creating an Clipboard intermediary file Icon s mi Tips and Tricks Menu Location e Theresolution ofthe spectrum image copied to the clipboard varies based on the size of the window on your screen in pixels If adjusting combinations of your window size and screen resolution do not allow you to produce images of a high enough quality you should consider using Export Spectrum Graphic Related Topics e Spectrum
78. 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 molecular weight of proline to three decimal places 115 130 Also enter a valid pH range of either 4 00 to 9 00 or 6 00 to 8 00 Enter noesy as the pulse sequence 8 Click OK 9 Set default 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 of the clusters near 4 1 3 4 3 3 and 2 3 ppm respectively and refine the fits 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 which you should remove before proceeding 11 Zoom to the cluster near 2 1 ppm select it and optimize the fit 12 Review the contributions of each of the peaks to the overall cluster shape Remove peaks that appear particularly small relative to the peaks immediately adjacent 6 peaks removed 13 Optimize the cluster and refine the fit 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 the fits 14
79. Line Ctrl Shift 1 Cmd Shift 1 Show Subtraction Line Ctrl Shift 2 Cmd Shift 2 Show Simulation Line Ctrl Shift 3 Cmd Shift 3 Show Selection Line Ctrl Shift 4 Cmd Shift 4 uu m Overlay Spectrum gt s E I Select Region Ctrl T Cmd T Linux Windows Mac OS X Simulation Menu Add Spin System Remove Spin System Add Spin Definition Remove Spin Definition Add J Modifier Edit J Modifier Remove J Modifier s Uncouple Split Group Ungroup Uncoupled Splits lt Previous Spin Definition Ctrl Shift Comma Cmd Shift Comma gt Next Spin Definition Ctrl Shift Period Cmd Shift Period Help Menu Contents F1 F1 Search ous Save Application Log X Activation Details eee mE About Chenomx NMR Suite ies M Oop 8 2 Quick Reference Guide 65 CHENOMX NMR SUITE USER MANUAL 8 3 Fitting 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 i
80. Location Compounds gt Scale Concentrations Icon s amp 1 Staratleastone compound 2 On the Compounds menu click Starred Compounds gt Scale Concentrations 3 Enterthe 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 Tips and Tricks e Ifyou 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 7 3 Profiling Tools 52 cH CHENOMX NMR SUITE USER MANUAL e Ifyou set the multiplication factor to zero all of the profiled compounds are set to 0 mM e Scale Concentrations does not affect compounds with unknown concentrations Related Topics e Starred Compounds on page 47 e Concentrations on page 49 Cluster Navigator The Cluster Navigator allows you to 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 This 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 c
81. 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 130 evomx CHENOMX NMR SUITE USER MANUAL eps encapsulated PostScript file exporting spectrum graphic exporting profiled compounds exporting profiled concentrations fid fid frequency domain size frequency filter ft2 generate cluster for region grouping J modifiers group peaks as cluster See encapsulated PostScript file PostScript file which contains image size and layout information 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 containing compounds from the currently open file that have been modified including concentrations transforms custom colors highlights and stars In Profiler refers to creating a tab delimited text file describing the concentrations stored in one or more profiled Chenomx spectrum files cnx The resulting file is suitable for use ina variety of statistical analysis and spreadsheet software See NMRPipe spectrum data See spectrum data The n
82. Review the contributions of each peak in the cluster at 1 979 ppm to the overall shape of the cluster a For pairs of near identical peaks remove one peak from each pair 8 peaks removed b For groups containing peaks much smaller than the immediately adjacent peaks remove the small peaks 13 more peaks removed 21 in total 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 of the remaining peaks contribute significantly to the optimized fit 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 fits of both clusters as needed 11 6 Tutorial Compound Builder 125 CHENOMX NMR SUITE USER MANUAL Now that the fit of the compound to the spectrum is satisfactory you can add proper transform windows to the clusters 18 Ifyou entered a valid pH range of 6 00 to 8 00 in the Compound Details set the following transform windows f g Cluster at 1 978 ppm Cluster at 2 011 ppm Cluster at 2 058 ppm Cluster at 2 339 ppm Cluster at 3 328 ppm Cluster at 3 412 ppm Cluster at 4 121 ppm 1 93 to 2
83. View Tools on page 20 e Export Spectrum Graphic on page 59 Send to Processor As you are working with a spectrum in Profiler you may notice that the phasing baseline Mooh File gt Send to Processor 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 Icons 8 baseline or other correction Send to Processor closes the current spectrum in Profiler and ae Ctrl J opens it in Processor retaining any changes you have made in Profiler Cmd J 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 e Chapter 6 Processor on page 27 7 5 Importing and Exporting Data 60 enomx Menu Location Icon s Hotkey s View Show Reference Panel Ctrl Shift R Cmd Shift R Menu Location Icon s File gt Spectrum Details CHENOMX NMR SUITE USER MANUAL 7 6 Information Tools While profiling spectra you can access extended information about the compounds in your Library as well as acquisition and sample information connected to the current spectrum You can also chang
84. XLUOUSUD Chenomx NMR Suite 5 0 Copyright 2003 2008 Chenomx Inc evomx CHENOMX NMR SUITE USER MANUAL Table of Contents Notices and Trademarks oe rc eter cinesi cnn cea Conv E REEL Rex rn RN ERES reste caniiy vii Ly Introduction pM ieii 1 PMiCIEMIEETM EUER 1 nns P 1 Linux 32 bit tier iet Ea to Eo denen a IDE A d n ELA 1 Ioardoseem m 1 1 2 Activation and Licensing eerie enero depen rdpn reir apu pe Rn kr ano Ned PEN pe E 1 1 3 Setting the Compound Library Folder sseseeeeeeneene 2 1 4 Importing the Chenomx Compound Packs sseseeeneee 3 2 Changes Since Chenomx NMR Suite 4 6 sssssssesssseeneeen meme 4 2 1 Signature Bullder s eene Eee Ee ur E rd itm SI 4 2 2 Spin Simulator 42i riesci deine dese isi aiai a aa P pa ariaa i iak aiia 4 2 3 Compound Builder CREER ca ee ee 4 2 4 Compound Library Folder iicet emitur Rene es inco peo xponu EAEAN 4 2 5 Compound Packs oO e E Duet erue i vU EU EE 5 2 6 Peak Shap Seeron oe araa E AR r ao niaii 5 2 7 Embedded Libraries iroso eor treni EE E aE 5 2 8 Editing Compounds in Your Library ssesseeeeemm mm 6 29 Quick Searches ees einn EE ORA TRRSME Eo kE eE 6 2 10 Versioned C MPOUNd Sirris issin eaaa emen men nennen nnne 6 2 11 J Modifiers ire erri hen e Noa ke e E Tha ug amr aE FED E a
85. Zoom Zoom Redo Zoom y Zoom Auto Zoom Ctrl F Cmd F je Zoom Increase Vertical Zoom 1 Zoom Decrease Vertical Zoom amp Show Reference Panel Ctrl Shift R Cmd Shift R D T Show Compound Set Panel Ctrl Shift K Cmd Shift K Show Cluster Navigator Ctrl Shift N Cmd Shift N Show Spectrum Line Ctrl Shift 1 Cmd Shift 1 Show Subtraction Line Ctrl Shift 2 Cmd Shift 2 Show Sum Line Ctrl Shift 3 Cmd Shift 3 Show Selection Line Ctrl Shift 4 Cmd Shift 4 He Change Columns ase HI I Select Region Ctrl T Cmd T Compounds Menu Selected Compound Submenu E Clear Concentration eee ba Clear gt Transforms scs a Clear gt Custom Color sss s Clear gt Highlight os ca amp Clear gt Star ss x Clear gt Everything Q Assign Custom Color D Update Profiled Version Ctrl U Cmd U 7 2 Quick Reference Guide 43 Enom CHENOMX NMR SUITE USER MANUAL Linux Windows Mac OS X Mi Set to Potential Concentration Ctrl P Cmd P lt Previous Cluster Ctrl Shift Cmd Shift gt Next Cluster Ctrl Shift Cmd Shift Starred Compounds and All Compounds Submenus E Clear Concentrations s a Clear gt Transforms ae ag Clear gt Custom Colors K Clear Highlights YE Clear Stars zs x Clear gt Everything D Update Profiled Versions M Set to Potential Concentrations Ha Scale Concentrations
86. able for Chenomx NMR Suite to import 3 3 Spectral Data Processing 9 CHENOMX NMR SUITE USER MANUAL 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 To allow Chenomx NMR Suite to read spectra processed using the Varian VNMR software package you should save the datdir folder for the spectrum using the svfph macro or copy it manually as described below The svfph macrois available on the Chenomx website at http www chenomx com support macros for instructions on how to install macros please consult your Varian documentation 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 fid is the folder that you need to access to open the spectrum using Chenomx NMR Suite Use the following commands cd vnmrsys data mydata fid 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 example expn would be exp
87. ack spectrum files cnx old Chenomx library files cnx1lib ZIP files zip or folders containing any of these file types 3 fnecessary choose the desired method of handling compounds that already exist in your library 4 Click Finish to import the selected compounds Tips and Tricks e Archiving compounds that already exist in your library places the archived compounds in a separate view in Library Manager Archived compounds may be added to 10 3 Library Tools 89 evomx CHENOMX NMR SUITE USER MANUAL Compound Sets when they are not automatically updating but not to Smart Compound Sets Library Manager searches through up to twenty levels of subfolders in each folder that you select If the compound sources that you expect to see do not appear try starting Import Compounds deeper in the folder structure Related Topics Compound Table on page 88 Show Archived Compounds on page 91 Rescan Compound Library on page 92 Compound Set Tools on page 93 Export as Compound Pack When you are collaborating with other people on a project you may have different versions of compounds in your library than your collaborator has in theirs Exporting a compound set creates a compound pack pack containing the set of actual compound signatures represented by the compound set Compound packs may be exchanged with other users of Chenomx NMR Suite and imported via Library Manager into a new com
88. actually a folder stored on your computer s hard drive containing Chenomx compound files xcpd corresponding to each of the compounds available for fitting spectra Each compound has properties like magnet frequency MHz and valid pH range telling you what sorts of spectra and samples itis best suited for You can then create lists called compound sets based either on arbitrary compounds that you have selected see Compound Sets on page 94 or on selection rules that you have defined see Smart Compound Sets on page 95 When you profile spectra in Profiler you have access to all ofthe compound sets that you have created all the time You can even change the contents of a compound set in Library Manager and the new contents will appear immediately in Profiler without the need to restart either module In any case no matter how many compound sets you create they are all still based on the same pool of compounds in your library with no duplicated signatures You can rename relocate or otherwise reorganize compound files xcpd within your compound library folder as you like The next time you use the software close all modules then open a new one the library folder will be rescanned and reindexed Once the scan is complete any changes will be visible immediately in Profiler and Library Manager 2 5 Compound Packs Sharing compound signatures with other users of Chenomx NMR Suite is easy with compound packs pack You can cre
89. al 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 Click View gt Show Subtraction Line to display the subtraction line green Several of the clusters in the imported simulation are quite simple Focus on refining the fits of simple clusters to the spectrum and then deal with the more complex cluster 11 Zoom to the cluster near 3 6 ppm using the Cluster Navigator and select it 11 6 Tutorial Compound Builder 122 evomx CHENOMX NMR SUITE USER MANUAL 12 Use the frequency and height controls to adjust the cluster blue to fit the spectrum black To further refine your fit adjust the cluster so that the subtraction line is as flat as possible When you are adjusting simple clusters you can get a very good approximate fit of the cluster automatically using optimization 13 Zoom to 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 fit and refine the fit 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 fit of a cluster it is important to ensure that the
90. an 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 Vis show Cluster Navigator 1 Make sure that the Cluster Navigator is visible and select a compound in the Ciri SAINEN Compound Table Cmd Shift N 2 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 Clickonacluster and drag along the Cluster Navigator to include adjacent clusters in the Spectrum View Related Topics e Spectrum View Tools on page 20 e Compound Table on page 44 e Concentrations on page 49 e Transforms on page 50 7 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 Set Panel The Compound Set Panel allows you to modify the contents of the Compound Table to 1 View Show Compound Set include any combination of the Compound Sets that you have created in Library Manager Menu Location x Panel The panel contains a list of every Compound Set that is currently defined Contents of the icon checked Compound Sets appear in the Compound Table Ctrl Shift K Ti
91. aph elements and some module specific settings How do I change preferences 1 Openthe Preferences module Select the module for which you would like to change preferences Make your desired changes Click OK De wn 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 Manual proxy configuration 3 Enter the IP address of your HTTP proxy server and the associated 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 change the line colors 1 Click the swatch box corresponding to the type of line whose color you would like to change 2 Clicka new color on the color palette 3 Click OK to accept the selected color How do set the default zoom 1 Selectthe Default Zoom check box 2 Inthe Default Zoom fields enter the default values in ppm for the range of the spectrum to display How do I specify the default file folder 1 Clickthe Always use this folder button 2 Click the default folder browse button 3 Locate the desired folder 4 Click Select to select the specified folder 5 11 Preferences 24 CHENOMX NMR SUITE USER MANUAL How do I specify the compound library folder 1 Click the Browse button 2 Locate the desired folder 3
92. 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 have just undone If you undo a change then make other changes you can no longer redo the change that was undone 5 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 l M 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 The Concentration Potential Color Highlights Stars and Transformed columns are only available in Profiler 5 8 Overlaying a Spectrum You can overlay Chenomx spectra cnx in Compound Builder and Spin Simulator to aid the fitting process How do I overlay a spectrum Menu Location View Overlay Spectrum 1 Click Overlay Spectrum ino Im 2 Locate the folder containing the spectrum that you would like to overlay and select the spectrum 3 Click Overlay 5 6 Undo and Redo 19
93. ars at 3 413 ppm and couples to protons 4a 4b and 5a Spin Definition 5 or SD5 g The signal for proton 2 appears at 4 121 ppm and couples to protons 3a and 3b Spin Definition 6 or SD6 Open Spin Simulator Overlay the proline spectrum called Samples Spin Simulator Proline cnx 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 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 is used throughout the tutorial for clarity Zoom in to SD6 4 121 ppm 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 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 Use the frequency width and height controls to match SD6 as closely as possible to the spectrum line If you need to adjust the J values for SD6 select the J modifier in the Spin D
94. as large as 2000 ppm 1000 to 1000 ppm e You can specify a maximum of 1000000 one million bins or a minimum of 1 e You can specify a minimum bin width of 0 00007 ppm and a maximum bin width equal to the width ofthe 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 e Profiling Tools on page 44 e Compound Set Tools on page 53 Export Spectrum Graphic When you prepare publications or presentations based on your work in Profiler you may need to include images illustrating the fitting process or particular regions ofthe spectrum You can export spectrum graphics at various resolutions and into a variety of formats including both bitmap and vector formats How do export an image of the current spectrum Menu Location Icon s File Export Spectrum Graphic m 1 Startthe Export Spectrum Graphic wizard 2 Choosea file format You can specify bitmap png or vector formats svg Svgz pdf ps eps 3 Choose the image size for bitmap formats or quality for vector formats based on your intended use of the image 4 Choose a folder and filename for the exported image 7 5 Importing and Exporting Data 59 CHENOMX NMR SUITE USER MANUAL Tips and Tricks e Ifyou plan to distribute the image via e mail or post it to a Web page use Portable Network Graphics png Scalable Vector
95. ate compound packs based on profiled compounds in Profiler or based on any compound set in Library Manager The resulting files can be imported into any other Chenomx NMR Suite 5 0 library and are compact enough to be attached to e mails sent through instant messaging clients or shared using any other method you may have available to share files with your colleagues 2 6 Peak Shapes The shapes of individual peaks clusters and compounds are now represented as filled in regions instead of simple lines with adjustment handles on each peak You can click and drag anywhere in the filled regions to interact with the associated items including peaks clusters compounds and sum lines 2 7 Embedded Libraries Profiled spectra cnx nolonger contain embedded copies of the libraries used to profile them Instead they store pointers to the relevant compounds in your library along with the actual profiled concentrations and transforms If you would like to update the profile you will need the signatures for the profiled compounds to be present in your library When you open spectrum files cnx from previous versions that contain embedded libraries the embedded data will be imported to your library folder Importing embedded compounds will not affect the fit of the spectrum file that you are opening as the original compound signatures will be used until you explicitly update them to the latest version Embedded compounds that are newer than th
96. ate the spectrum more easily Reference Panel Displays additional information for the compound currently selected in the Compound Table including structure molecular weight CAS RN and so on 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 00 Linux Windows Mac OS X File Menu Open Ctrl O Cmd O Open Recent Close Ctrl W Cmd W Save Ctrl S Cmd S Save As a Send to Processor Ctrl J Cmd J Open Library Manager Ctrl B Cmd B Import Profile Export gt Profiled Compounds pack Export gt Profiled Concentrations txt Export gt Spectrum Graphic Spectrum Details as ics Euer tev eugpsu5 trccce Preferences I Exit i oe Edit Menu Undo Ctrl Z Cmd Z C Redo Ctrl Y Cmd Y m Copy Spectrum Image to Clipboard View Menu Concentration Units e ae 7 2 Quick Reference Guide 42 evxomx CHENOMX NMR SUITE USER MANUAL Linux Windows Mac OS X X Scale Y Scale e ol Zoom Show Entire Spectrum Ctrl Cmd a Zoom Set Zoom Ctrl M Cmd M h Zoom gt Undo
97. ave 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 76 e Remove Selected Peaks on page 78 e Adjusting Peaks on page 78 e Grouping Peaks as a Cluster on page 79 e Optimize Selected Peak Shapes on page 79 e Generate Cluster for Region on page 80 e Transform Windows on page 81 9 3 Fitting Tools 77 CHENOMX NMR SUITE USER MANUAL e Cluster Navigator on page 82 Remove Selected Peaks As you develop a compound signature you may need to remove one or more peaks from the signature to refine or simplify the signature You can remove one or more selected peaks from the current signature including peaks in different clusters whole clusters or multiple clusters How do I remove peaks Menu Location Icon s Hotkey s compound es Selected 1 Select the peaks or clusters that you would like to remove y 2 Click Remove Selected Peaks Delete Tips and Tricks Delete e You can remove multiple peaks or clusters by selecting them via the Spectrum View or the Information Panel e Right click ona selection in the Spectrum View or Information Pane and select Remove Peaks to remove the selected peaks Related Topics e Add Peak on page 76 e Selecting Peaks and Clus
98. based on the observed position of a single peak see Figure 6 1 on page 31 while the formula used for both imidazole and creatinine uses the distance between the two observed peaks see Figure 6 2 on page 31 H 2 pKa 4 ml lo 2 2 p p 810 AD Amaz Figure 6 2 Equation to calculate spectrum pH from the positions of two peaks pKa is 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 is derived from a similar equation published recently see citation below The two peak equation was developed internally by Chenomx 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 and a pair of green lines at mid frequency creatinine and an 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 1 Switch to the pH Editor
99. basic building blocks of the models created by Spin Simulator A spin definition consists of three basic pieces of information A 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 66 How do add a new spin definition 1 Openthe Add Spin Definition dialog 2 Enteranumber of protons starting center in ppm and starting width in sw These values can be changed later 3 Click OK How do edit a spin definition 1 Select the spin definition by clicking on it in the Spectrum View or selecting its Spin Definition Tab in the Spin Definition Pane 2 Dooneor more ofthe 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 8 3 Fitting Tools 67 evomx CHENOMX NMR SUITE USER MANUAL 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 of the spin definition
100. by two much shorter peaks These groups can also be replaced by single peaks with little effect on the quality of the fit 20 Find all of the groups of three peaks as described above and remove the two flanking peaks from each group 6 groups 12 peaks removed 21 Optimize the fit 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 fit of the compound to the spectrum is satisfactory you can add proper transform windows to the clusters 22 Ifyou entered a valid pH range of 6 00 to 8 00 in the Compound Details set the following transform windows 11 6 Tutorial Compound Builder 123 Enom CHENOMX NMR SUITE USER MANUAL a Cluster at 0 978 ppm 0 95 to 1 00 ppm b Clusterat 1 031 ppm 1 00 to 1 05 ppm c Cluster at 2 263 ppm 2 21 to 2 31 ppm d Cluster at 3 605 ppm 3 57 to 3 62 ppm 23 If you entered a valid pH range of 4 00 to 9 00 in the Compound Details set the following transform windows Cluster at 0 978 ppm 0 92 to 1 00 ppm b Clusterat 1 031 ppm 0 99 to 1 05 ppm c Cluster at 2 263 ppm 2 16 to 2 31 ppm d Cluster at 3 605 ppm 3 50 to 3 64 ppm 24 Savethe compound file If you would like to review the sample fit for valine you should not replace the file called Samples Compound Builder WNValine xcpd
101. ceed Automatic phasing often provides reasonable results For the best results visually inspect the automatic results and refine them as needed The water peak often does not phase properly with the rest of the spectrum so you should focus on other signals in the spectrum instead Phase angles for the sample spectrum are near 54 zero order and 2 first order Breakpoints are normally placed directly on the spectrum line Hold down the Control or Command key while clicking to place breakpoints at arbitrary positions If your spectrum has poor phasing or baseline correction finding the CSI automatically will not work you should readjust the phasing and baseline correction before proceeding CHENOMX NMR SUITE USER MANUAL e Clear the Line Broadening check box e Set Zero Fill to to Automatic if it is not set already e Clear the Phasing check box e Clear the Auto Baseline Correction check box e Clear the Delete Water Region check box e Click the OK button Adjusting the Spectrum Phasing 4 5 7 Switch to Phasing mode Click the Auto button Click on Very Fine to make small adjustments to the phasing Drag the sliders for zero order and first order phase angles until the peaks in the spectrum appear symmetrical 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 Correcti
102. ch can be very helpful For this tutorial start at the right most edge of the spectrum and move to the left Fitting Compounds with Overlap 5 6 Inthe Compound Table select pantothenate and set itto its potential concentration Zoom in on the two single peaks for pantothenate near 0 90 ppm These peaks correspond to methyl groups in the structure of pantothenate Methyl groups can be very useful in setting an appropriate concentration for a compound as they are usually easy to locate Click and drag the two peaks 0 88 and 0 92 ppm to best fit the corresponding peaks in the spectrum You can use the frequency and height controls on the axes to restrict the movement of a peak to only one dimension Clickthe location ofthe next pantothenate cluster 2 4 ppm in the Cluster Navigator Use the frequency control on the horizontal axis to match the signature blue to the spectrum black Although the left most peak ofthis cluster overlaps with 2 oxoglutarate the remaining two peaks provide enough information to establish an appropriate location for the cluster 11 3 Tutorial Profiler 105 evomx CHENOMX NMR SUITE USER MANUAL 10 11 12 13 14 15 16 17 18 19 20 21 22 23 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 co
103. 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 asa cnx file The compound that you star remains starred when you next open the file until you clear the stars Related Topics e Compound Table on page 44 e Custom Colors on page 46 e Highlighted Compounds on page 46 e Concentrations on page 49 e Transforms on page 50 e Potential Concentrations on page 51 e Scale Concentrations on page 52 Update Profiled Versions Several Compounds on page 54 7 3 Profiling Tools 47 CHENOMX NMR SUITE USER MANUAL 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 fit Quick Searches allow you to temporarily 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 limit the compounds visible in the Compound Table Icon s Hotkey s X Ctrl L Cmd L 1 Clickthe binoculars icon at the left edge o
104. ctrum in megahertz MHz Concentration of the compound in the sample spectrum in millimoles per litre mM 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 Valid pH Range pH range over which you expect the compound signature and specifically the transform windows to be valid Pulse sequence used to acquire the sample spectrum that you would like to use as an reference overlay for the compound signature UUID Universally Unique Identifier used to uniquely identify a particular signature in your compound library 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 quantification results you should 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 fyouintend to use concentration units of milligrams per decilitr
105. culates a compound s potential concentration 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 taking into account all possible transform values that can apply to each cluster The value is intended to act as a guideline only How do set a compound to its potential concentration Menu Location Icon s Hotkey s Compounds Selected Compound Set to Potential Concentration vi Ctrl P Cmd P 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 2 Onthe Compounds menu click Selected Compound gt Set to Potential Concentration or right click on the compound and select Set to Potential Concentration from the context menu 7 3 Profiling Tools 51 Enom CHENOMX NMR SUITE USER MANUAL How do I set a compound to its potential concentration Compounds gt Starred Menu Location Compounds gt Set to Potential Concentration Icon s Ni 1 Staratleastone compound 2 Onthe Compounds menu click Starred Compounds Set to Potential Concentration How do I set all compounds to their potential concentrations 1 OntheCompounds menu click All Compounds Setto Potential Concentration Compounds All Compounds Set to Potential Concentration Icon s ME Menu Location
106. cy 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 Open Spectrum Details 2 Click anywhere in the Comment field to place a text cursor in the field 3 Make any desired changes 4 Click the Accept button to apply your changes or click the Cancel button to discard them Tips and Tricks e You must save the spectrum in order 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 e 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 Importing Spectra on page 16 e CSI Editor on page 29 6 3 Information Tools 33 evomx Menu Location Icon s Hotkey s Processing Phasing pa Ctrl Alt 1 Cmd Alt 1 CHENOMX NMR SUITE USER MANUAL e pH Editor on page 30 6 4 Processing Tools Processor appli
107. d Menu Location Compound Clear Custom Color Icon s a 1 Select the compound in the Compound Table 2 Click Clear Custom Color Tips and Tricks 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 Related Topics e Compound Table on page 44 e Highlighted Compounds on page 46 e Starred Compounds on page 47 Highlighted Compounds It is often useful to display several different compounds at the same time while fitting especially when you are working in heavily overlapped area Highlighting a compound allows you to pin itto the graph so that it remains visible regardless of which compound you have selected in the Compound Table In combination with custom colors and exporting spectrum graphics highlighting can also help you to prepare snapshots of your fit that are suitable for publication How do I highlight a compound 1 Click the check box for the compound in the Highlighted column 9 of the Compound Table How do I clear a highlighted compound Compounds Selected Compound gt Clear gt Highlight Icon s Menu Location 1 Select the compound in the Compound Table 2 Inthe Compounds menu
108. d Shift I Help Menu Contents F1 F1 2 Search 9 2 Quick Reference Guide 74 CHENOMX NMR SUITE USER MANUAL Linux Windows Ld Save Application Log E Activation Details 9 About Chenomx NMR Suite 9 3 Fitting Tools Compound Builder provides you with a variety oftools to help you create accurate compound signatures by adding manipulating and removing peaks grouping peaks into clusters and defining ranges within which clusters are allowed to move You can also generate arbitrary clusters to fit the overall lineshape of a region or optimize peaks to better fit the spectrum New Compound New Compound creates a new compound file xcpd The new compound file has the Menu Location File New Compound default Compound Details including a magnet frequency of 800 MHz and a sample concentration of 5 mM Tips and Tricks e You need to save the new file in order to retain changes that you have made Related Topics e Overlaying a Spectrum on page 19 e Compound Details on page 84 e The new compound file does not have an overlaid spectrum You should overlay a spectrum before you continue creating a compound signature Importing allows you to use an existing spin simulation xss or legacy compound album cca to guide creating a new compound file How do import a spin simulation or compound album Icon s P Ctrl N Hotkey s Cmd N Import Men
109. d Tricks e Ifyou restored files from your operating system s Recycle Bin or Trash folder back into your compound library folder to recover compounds that you inadvertently 10 3 Library Tools 92 evomx CHENOMX NMR SUITE USER MANUAL removed from the library you may need to rescan the library to make the compounds visible again e Changes that you make to the library from within any module of Chenomx NMR Suite including Compound Builder and Library Manager appear immediately in any other modules that may be open You do not need to rescan the library to detect these types of changes Related Topics e Compound Table on page 88 e Import Compounds on page 89 e Show Archived Compounds on page 91 e Remove Selected Compounds from Library on page 92 10 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 Set Panel The Compound Set Panel contains a list ofthe currently defined Compounds Sets and allows you to interact with them by displaying the contents of Compound Sets adding compounds to them or editing filters for Smart Compound Sets The Compound Set Panel also contains the Compounds setand the Archived Compounds s
110. 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 assigned to a compound by Chenomx staff and used to uniquely identify the compound in the Chenomx compound library Group of peaks that can be moved or otherwise adjusted 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 used in Compound Builder and Profiler to adjust the Spectrum View to include specific clusters present in the current compound See spectrum file See license file Module in Chenomx NMR Suite used to prepare and modify compound signatures xcpd in your Library Information about a compound signature created in Compound Builder Some of the information is displayed directly in the reference panel some is used to access other information for display in the reference panel and some is used to index 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 p
111. dicator of the quality of your fit 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 fucose clusters near 1 2 ppm to fit the spectrum Use the cluster at 1 24 ppm to establish the concentration for fucose Return to the fucose cluster near 3 4 ppm and use the frequency control to match it to the spectrum using the sum line to evaluate your progress Select pantothenate again and use the Cluster Navigator to view the cluster near 3 5 ppm Adjust the pantothenate cluster at 3 51 ppm to fit the spectrum Use the frequency control Move on to the pantothenate cluster near 4 0 ppm and use the frequency control to fit the cluster to the nearest peak in the spectrum 11 3 Tutorial Profiler 106 evomx CHENOMX NMR SUITE USER MANUAL 24 25 26 27 28 29 30 31 32 33 34 35 36 37 The fitted peak for pantothenate in this region does not completely fit the area available due to overlap with serine Once you have fit serine this peak will fit better Inthe Compound Table set glycolate and serine each to their potential concentration and then select serine Use the Cluster Navigator to display the serine cluster near 3 8 ppm and adjust it to fit the spectrum u
112. download Ifyou have not received the compound packs that you have licensed please contact Chenomx Technical Support at 1 780 432 0033 or support chenomx com To import Chenomx Compound Packs T Save your Chenomx compound packs pack to a folder accessible to the computer on which you have installed Chenomx NMR Suite Open the Library Manager module of Chenomx NMR Suite On the Compounds menu click Import Click the Browse button and navigate to the folder in which you saved your Chenomx compound packs pack Select the compound packs that you would like to install and click Choose Files Click Next If you would like Library Manager to automatically create compound sets for the imported compounds select Create associated compound sets Creating compound sets is strongly recommended If you prefer to simply import the compounds clear the Create associated compound sets check box You will need to create compound sets later to use the imported compounds in Profiler Click Finish 1 4 Importing the Chenomx Compound Packs 3 Chapter 2 Changes Since Chenomx NMR Suite 4 6 Chenomx NMR Suite 5 0 has been rewritten in almost every area compared to previous releases Many new features have been added some old features behave a little differently while others have been removed or replaced entirely To help you move to the new release more smoothly here are some ofthe changes that may affect how you
113. e mg dL in Profiler you should enter a molecular weight 9 4 Information Tools 84 CHENOMX NMR SUITE USER MANUAL 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 in order to retain new or changed Compound Details Related Topics e Fitting Tools on page 75 e Reference Panel on page 83 e Chapter 10 Library Manager on page 86 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 allowing you to access the edit dialog for any clusters or peaks you may have selected You can also select peaks and clusters directly in the Information Panel allowing more precision than selecting them from the Spectrum View directly Tips and Tricks e You can select multiple peaks 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 overlaid the Information Panel indicates that your compound signature is in the default environment When you overlay a spectrum the environment changes to
114. e 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 Related Topics Preferences on page 24 e Fitting Tools on page 75 e Compound Details on page 84 9 4 Information Tools 83 evxomx CHENOMX NMR SUITE USER MANUAL Compound Details Using Compound Details you can associate information with compound signatures that Menu Location Icon s File gt Compound Details you create The information that you enter allows you to use the signature with appropriate spectra display correct information in the Reference Panel calculate accurate concentrations and manage the contents of your compound library effectively Table 9 1 Compound Details Required Compound Name Compound Author Magnet Frequency MHz Sample Concentration mM Name of the compound as you would like it to appear in the Compound Table in Profiler Author of the compound signature as you would like it to appear in the Compound Table in Profiler Frequency of the acquired NMR spe
115. e applies a cubic spline baseline correction based on automatically determined breakpoints Remove the water region from the spectrum during the import process Reverse your spectrum horizontally You generally need to reverse all spectra acquired with a particular experimental setup on a particular instrument 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 you should save often 5 3 Saving a File 17 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 pore How do I save a file with a different file name 1 Click Save As 2 Locate the folder in which you would like to save the spectrum 3 Inthe File 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 overlaid spectra in the saved files 5 4 Closing a File 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
116. e deconvolution 37 reverse spectrum 39 water deletion 38 profiled compounds 44 46 47 49 50 52 56 57 profiling techniques basic fit 110 best guess fit 113 no fit 114 subtraction line fit 110 sum line fit 111 water suppression 112 proline 117 124 126 Q quick search 48 89 R redo zoom 21 reference deconvolution 37 DSS TSP satellites 37 target linewidth 37 reference panel 61 83 relaxation delay 9 remove compound from compound set 94 compound from library 92 J modifier 69 overlaid spectrum 19 peak 78 spin definition 67 spin system 66 rename compound set 97 rescan compound library 92 reverse spectrum 39 rolling 35 S sample concentration 84 sample preparation 8 scalable vector graphic svg 59 scale concentrations 52 select cluster 77 peak 77 region 22 selection line 23 CHENOMX NMR SUITE USER MANUAL send to Compound Builder 91 Processor 60 Profiler 40 set to potential concentration 51 zoom 20 show entire spectrum 20 Signature Builder 4 simulation 66 details 71 file xss 16 66 75 frequency 71 line 23 new 66 spin definition 67 spin system 66 67 smart compound set 93 95 97 edit 95 new 95 smiles 35 spectral binning 58 bin label 58 bin size 58 bin width 58 binning target 58 exclude region 58 normalization 58 output options 58 total area 58 spectral width 9 spectrum Bruker spectrum file fid 16 file cnx
117. e same compounds or with compounds that no longer exist These discrepancies between your current library and the fit in a spectrum file are marked with status icons like amp for changed compounds or for missing compounds You can update a particular profiled compound to reflect the latest version present in your library This allows you to update compounds in a controlled fashion revising your fit one compound at a time as needed How do I update a single profiled compound 1 2 Selectthe profiled compound that you would like to update in the Compound Table If you do not see any profiled compounds in the Compound Table select the Profiled Compound set in the Compound Set Table Click Compound Selected Compound Update Version Tips and Tricks This operation only updates the compound that you have selected in the Compound Table You can also update a single profiled compound via a context menu Right click on the compound in the Compound Table and click Update Version Related Topics Compound Table on page 44 Update Profiled Versions Several Compounds on page 54 Update Profiled Versions Several Compounds If you prefer you can update many compounds at once instead of updating one at a time You can update all profiled compounds in one operation or update only profiled compounds that you have starred 7 4 Compound Set Tools 54 CHENOMX NMR SUITE USER MANUAL How do I update all
118. e spin definition or coupled linking the spin definition to another one via its coupling constant Coupled J modifiers allow more accurate simulations as Spin Simulator can use them to calculate higher order coupling effects accounting for tenting and other complex behaviour 8 3 Fitting Tools 69 Enom Menu Location Icon s Compound Add J Modifier P Menu Location Icon s Compound gt Edit J Modifier 3 Menu Location Icon s Compound Remove J Modifier ES Menu Location Icon s Compound Uncouple CHENOMX NMR SUITE USER MANUAL How do 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 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 Open the Add J Modifier dialog Enter a J value for the new J modifier in Hz Select Coupled and select the spin definition to which you would like to link Click OK u e w N How do I edit an existing J modifier 1 Selecta spin definition 2 Selecta J modifier that you would like to edit 3 Open the Edit J Modifier dialog 4 Make your desired
119. e the concentration units that appear in the Compound Table and any exported profiles Reference Panel The Reference Panel displays information specific to the compound that you have selected in the Compound Table This 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 of the compound that you are fitting and better understand the signature and behaviour of the compound in your spectra 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 of the 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 You can open the Reference Panel for a specific compound by double clicking the compound in the Compound Table Double click again to close the Reference Panel 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 Related Topics Preferences
120. ectrum to a certain extent 141 Index A ACD Labs 9 acquisition time 9 activation 1 key 1 license 1 license file cnxlic 1 add J modifier 69 peak 76 selected compounds to Compound Set 94 spin definition 67 spin system 66 animated zoom 24 annotations custom color 44 46 highlight 44 46 star 44 47 application log vii archived compound 91 auto zoom 21 automatic baseline correction 35 automatic phasing 34 automatically update compound set 96 B baseline correction 35 automatic 35 breakpoint 35 frowns 35 rolling 35 smiles 35 wings 35 basic fit 110 best guess fit 113 bin label 58 size 58 width 58 binning target 58 breakpoint 35 Bruker processed data 1r 16 spectrum file fid 16 C change columns 19 Chenomx file types compound album file cca 75 compound file xcpd 16 75 compound pack pack 3 5 57 license file cnxlic 1 simulation file xss 16 66 75 spectrum file cnx 16 39 Chenomx Technical Support vii clear concentration 49 transform 50 transform window 81 cluster generate for region 80 group peaks as 79 list 85 navigator 53 82 select 77 comment 33 compound add to Compound Set 94 album file cca 75 archived 91 author 84 details 84 file xcpd 16 75 filter in selected region 48 filter near x xx ppm 48 ID 84 line 23 name 84 new 75 pack pack 3 5 57 remove fro
121. efault state including concentrations transforms custom colors highlights and stars will appear in the Profiled Compounds set and will appear in bold in the Compound Table 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 Related Topics e Custom Colors on page 46 e Highlighted Compounds on page 46 e Starred Compounds on page 47 e Quick Searches on page 48 e Concentrations on page 49 e Potential Concentrations on page 51 e Compound Set Tools on page 53 e Export Profiled Concentrations on page 56 e Concentration Units on page 62 7 3 Profiling Tools 45 Enom CHENOMX NMR SUITE USER MANUAL 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 assign a custom color to a compound Compounds gt Selected Menu Location Compound gt Assign Custom Color Icon s e 1 Selectthe compound in the Compound Table Open the Assign Custom Color dialog 2 3 Choose a color to assign to the compound using the displayed color palette 4 Click OK How do I clear a custom color from a compound Compounds Selecte
122. efinition Panel and use the J Value Editor appearing under the Spin Navigator to fine tune the J value 11 5 Tutorial Spin Simulator 118 evomx CHENOMX NMR SUITE USER MANUAL 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 definitions 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
123. eir equivalents in your library will replace the older verson while those that are older will be added to the Archived Compounds list Embedded compounds with no equivalentin your library will simply be imported Any new compounds will then be available to be added to Compound Sets for use in Profiler 2 5 Compound Packs 5 CHENOMX NMR SUITE USER MANUAL 2 8 Editing Compounds in Your Library You can directly edit compounds in your library Double click on any compound in the Compound Table in Library Manager to send itto Compound Builder for revision Alternately double click any compound file xcpd in your compound library folder to open it in Compound Builder When you save the compound save it over the original file to replace the original in your library See Universally Unique Identifiers UUID on page 7 for more details 2 9 Quick Searches Filtering the contents of your Compound Tables is easier and more powerful than ever Quick Searches allow you to type in text searches acetate frequency searches 92 30 and even frequency range searches 2 30 to 4 19 helping you find your favorite compounds quickly and easily 2 10 Versioned Compounds Compounds in your library are now versioned using a combination of a universally unique identifier see Universally Unique Identifiers UUID on page 7 for more details and a modification date The combined information allow Chenomx NMR Suite to track and update individual
124. epresents a subtraction ofthe current fit from the spectrum or overlay line and appears green by default Show Sum Line Toggles the display ofthe sum line in Profiler The sum line represents the total shape of all ofthe profiled compounds in the current spectrum and appears red by default Show Compound Line Toggles the display ofthe compound line in Compound Builder The compound line represents the total shape of all of the clusters in the current compound and appears red by default Show Simulation Line Toggles the display ofthe simulation line in Spin Simulator The simulation line represents the total shape of all of the spin definitions in the current simulation and appears red by default Show Selection Line Toggles the display ofthe selection line in Profiler Compound Builder and Spin Simulator The selection line represents the shape ofthe currently selected compound peak cluster or spin definition and appears blue by default 5 10 Display Options 23 evomx Menu Location Icon s File gt Preferences CHENOMX NMR SUITE USER MANUAL Tips and Tricks e You can change the colors of the various graph elements noted above as well as that of the background and zoom box in the Preferences for the appropriate module Related Topics Preferences on page 24 5 11 Preferences In Preferences you can specify default folders default settings for the Spectrum View colors of various gr
125. er ssseeseeeeeeme ee 121 Introductio erc EUER 121 Part I Simple Compound 0c ceeeee cence eee ee eee eee eee eee mene 121 Part II Complex Compound esserne eain sean een 124 11 7 Tutorial Library Manager c ccceceee cece nett eee ee eee eee menn 126 Introduction eic rte peek ete Eri a AEE G EEA 126 Importing Compounds 2 chassis vcciedexdondsntvecdendiucceiccescotiedixacndeai eaces 126 GlOSSaEy zit eoi unsafe SRI RE ELDER I MM CIL EPI a 128 nS 142 vi evomx Menu Location Icon s Help gt Save Application Log kd CHENOMX NMR SUITE USER MANUAL Notices and Trademarks Developed by Chenomx Inc 2003 2008 Chenomx Inc All rights reserved No copying or reproduction allowed without express written permission Technical 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 t
126. er 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 available lines including the spectrum spectrum overlay sum compound simulation subtraction CSI and highlight 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 matching the selection line blue to the spectrum line black 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 128 Enom CHENOMX NMR SUITE USER MANUAL bin Bruker processed spectrum data chemical shift and shape indicator chemical shift equivalent Chenomx compound ID cluster Cluster Navigator cnx cnxlic Compound Builder compound details compound file compound library compound line compound pack 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
127. er you will create 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 1CH3 O wo NH OH 11 6 Tutorial Compound Builder 121 evomx CHENOMX NMR SUITE USER MANUAL 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 windows and the associated valid pH range For the best results when you integrate the compound into your library you also need to add some descriptive metadata about the compound Creating a Compound Signature for Valine 1 Open Compound Builder 2 Import the 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
128. es each processing step as a layer 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 spectrum as it appeared before processing in other software you need to import the raw data fid jdf fid directly Phasing Phase correction or phasing allows you to correct for phase shifts that may have occurred during data acquisition You can recognize phase shifts in a spectrum as 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 You should adjust phasing before applying any other processing layers to your spectrum like baseline
129. es is an important technique for fitting large series of similar spectra efficiently 7 5 Importing and Exporting Data 57 evomx CHENOMX NMR SUITE USER MANUAL How do import a profile from another spectrum Menu Location Icon s File gt Import Profile g 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 fits of the current spectrum that you may have done before you imported the profile Related Topics e Profiling Tools on page 44 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 of regions or bins allowing analysis of the integrated area ofthese bins instead ofthe raw spectral data Profiler allows you to 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 Menu Location Icon s Tools Spectral Binning 1 Startthe Spectral Binning wizard 2 Choose the source spectra for binning and specify a target folder for the resulting binned data You ca
130. et since its transform windows are wider Text Filters You can filter the Compound Table based ona simple text search by typing the text to search for in the empty text box at the top right corner of the Compound Table This can help you look for a particular compound or a group of compounds with similar names like all compounds containing acetate You can also use text filters to type in frequency searches see Frequency Filters on page 108 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 92 75 to 4 30 without the quotes Compound Lists Alist of compounds known to occur in samples ofthe type that you are analyzing can be an invaluable tool to guide your fit of a spectrum 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 a list 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 fitting process 2 Oxoglutarate DSS Chemical Shape Indicator Pyruvate 3 Indoxylsulfate Formate Serine 4 Hydroxy 3 methoxymandelate Fucose Taurine Acetate Fumarate Threonine Alani
131. et when enabled allowing you to review the complete contents of your library as well as earlier versions of compounds that you have updated How do display the contents of a Compound Set 1 Selectthe set in the Compound Set Panel The contents ofthe set appear in the Compound Table Tips and Tricks e You can drag compounds onto a Compound Set in the Compound Set Panel to add them to the set This does not apply to Smart Compound Sets e You can rename Compound Sets and Smart Compound Sets directly in the Compound Set Panel Click on the name ofa 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 Set Panel Related Topics e Library Tools on page 88 e Export as Compound Pack on page 90 e Compound Sets on page 94 e Smart Compound Sets on page 95 10 4 Compound Set Tools 93 evomx Menu Location File gt New Compound Set Icon s D Ctrl N Hotkey s nin md Compounds gt Add Selected ami linee Compounds to Compound Set Compounds Remove Selected Compounds from Compound Set Menu Location Hotkey s Delete CHENOMX NMR SUITE USER MANUAL e Rename Compound Sets on page 97 e Delete Compound Sets on page 97 Compound Sets You may need to create a Compound Set that does not change as you add new compounds to your library
132. ew of the Compound Table based on entered text Results can be shown for matches to any or all of compound name compound comment compound ID or location in the spectrum in ppm 135 CHENOMX NMR SUITE USER MANUAL evomx R reference deconvolution Reference Panel relaxation delay rescan compound library residual binning reverse spectrum sa scalable vector graphics select region selection line send to Compound Builder send to Processor Processing layer available in Processor Used to reconstruct an ideal spectrum by removing lineshape distortions caused by systematic variations in the magnetic field of the spectrometer 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 inan 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 In Library Manager allows a user initiated rescan of the folder in which compound signatures are stored usually to ensure that changes made to the folder directly via the file system are properly reflected in the library Alternative to restarting Library Manager which rescans the library folder on startup Var
133. f 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 something here the default search type is All 2 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 3 Click the clear button 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 I search for compounds near a single frequency 1 Right click on the spectrum and click Filter for Compounds Near x xx ppm 2 Click the clear button 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 1 Use the Select Region tool to select a region of the spectrum 2 Right click on the selected region and click Filter for Compounds in Selected Region 3 Click the clear button at the right edge of the search box to cancel the search and restore the full list of compounds 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 e You can click repeatedly anywhere under the sum line red in the Spectrum View to cycle through the compounds cont
134. fore try a small dataset of five or ten spectra first before moving on to larger datasets The time needed for the smaller 7 5 Importing and Exporting Data 58 evomx CHENOMX NMR SUITE USER MANUAL dataset will help you to more accurately estimate the time needed to complete a binning session e Ifyou choose one or more folders as the source binning only includes spectra both directly in the specified folders and in subfolders of the specified folders e Ifyou do not explicitly specify a target folder output files are created in the folder containing your source spectra e 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 Inorder to do residual binning each of the source spectra must have been analyzed in Profiler and must contain at least one compound with a defined concentration e Excluding regions from a binning dataset can help you to remove the influence of interfering or confounding signals e 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 e 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
135. ger than the J value for the coupling to SD1 The resulting values are 7 57 Hz to SDO and 6 87 Hz to SD1 27 Usethe frequency width and height controls to match SD3 as closely as possible tothe spectrum line Since the spin definition overlaps with other on the right hand side use the peaks on the left hand side to guide your adjustments Most ofthe 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 have seen about 13 Hz 28 Adda J modifier to SD1 and couple it to SDO using a J value of 13 Hz 11 5 Tutorial Spin Simulator 120 Enom You can only complete the o Compound Builder tutorial if you have purchased the Professional edition of Chenomx NMR Suite or if you are using a time limited trial version of Chenomx NMR Suite CHENOMX NMR SUITE USER MANUAL 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
136. h the spectrum Since no information is available to guide a fit of 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 Isoleucine 9 uv Cluster 0 right Cluster 1 left 0 04 0 03 M MN ENT Au atl Ww J vA T 0 00 r 4 31 1 00 e 0 90 Figure 11 10 The doublet near 1 ppm provides enough information to set a concentration for isoleucine and the triplet near 0 92 ppm allows some confirmation of the identity It is reasonable that isoleucine is present at or near 9 uM 11 4 Tutorial Targeted Profiling 114 CHENOMX NMR SUITE USER MANUAL Isoleucine 9 um Cluster 5 2 qluster 4 Cluster 3 Cluster 2 B 0 02 V n MAN A M M cuv k Anila gh N Sy M eme gio NARI MM 0 00 0 0 A lt gt ES L Lr A E DM A 45 365 3 60 2 00 1 95 1 50 1 45 1 30 128 1 20 Figure 11 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 11 5 Tutorial Spin Simulator Introduction o You can only complete the Spin You can use the Spin Simulator module to create spin simulations
137. he Profiled Compounds set is selected If you still do not see any transformed compounds then the current file may not contain any transformed compounds 2 Inthe Compounds 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 e You can hover the mouse cursor over any cluster or its transform adjustment triangle on the horizontal axis to see the transform applied to the cluster The information appears in the top right corner of the Spectrum View If the cluster is not transformed the display reads Cluster is unchanged e To clear all of the transforms for the current spectrum select Compounds gt All Compounds gt Clear Transforms Toclear transforms only for starred compounds select Compounds gt Starred Compounds gt Clear Transforms e You can see which compounds have been transformed by turning on the Transformed column in the Compound Table Related Topics e Spectrum View Tools on page 20 e Compound Table on page 44 e Starred Compounds on page 47 e Quick Searches on page 48 e Concentrations on page 49 e Compound Set Tools on page 53 e Transform Windows on page 81 Potential Concentrations The potential concentration of a compound in Profiler is an estimate of the upper limit of the compound s concentration Profiler cal
138. he application log file If you do not specify a different name the file is saved as application log 4 Click Save 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 stored 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 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 ofthe 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 vii CHENOMX NMR SUITE USER MANUAL Windows Windows NT Windows XP Windows 2000 and Windows Vista are either trademark
139. iation 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 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 used to mark a specific region of the spectrum in the Spectrum View Used to provide more precise zooming to define frequency ranges for quick searches to mark clusters peaks or spin definitions for selection to mark a region in which to generate a new cluster and so on 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 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 allow modification of the processing layers CSI settings spectrum pH or spectrum details The details of the current profile concentrations transforms etc are retained even if the spectrum is then saved from Processor and closed 136 evomx CHENOMX NMR SUITE USER MANUAL send to Profiler si
140. igating use the Cluster Navigator to verify that the other clusters for the compound also appear to fit reasonably well then proceed to determine an appropriate height and or appropriate transforms for the clusters of the compound see Cluster Navigator on page 53 Concentrations on page 49 and Transforms on page 50 8 Ifthe fit does not appear reasonable reset the concentration of the compound to unknown see Concentrations on page 49 9 Continue evaluating the remainder of the compounds in the list 10 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 48 4 4 Fitting Overlapped Regions in a Spectrum For all but the simplest spectra you need to fit compounds whose signatures overlap Approaches to fitting these overlap regions are as varied as are the number of people fitting them but the general guidelines below may help you to develop your own strategy As with your more general approach to fitting spectra a consistent strategy for fitting overlap regions gives you more consistent results For more details on this and other fitting strategies see Tutorial Targeted Profiling on page 108 To fit compounds in an overlapped region of the spectrum 1 Identify likely compounds contributing to an overlapped region see Identifying Compounds on page 12 2 Evaluate each compound for the presence of additional
141. ing spectra in Processor does not alter your original spectral data Every processing effect that you add to a spectrum behaves as alayer that modifies the display of your original data All ofthese effects are completely reversible and are tracked in the Processing History panel 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 of the layers that you have already applied The Processing History maintains a list of every processing layer 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 details for the Preprocessing layer appearing atthe bottom ofthe 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 Openthe Processing History panel if itis not already open 2 Clickthe name ofa processing layer to review its associated parameters they appear in the Detai
142. justing Peaks on page 78 e Generate Cluster for Region on page 80 Generate Cluster for Region You may need to quickly create a compound signature that will allow you to verify that the compound is present in a spectrum without necessarily allowing the full range of flexibility that a chemically accurate fit affords You can create these limited use signatures using automatically generated clusters Generated clusters lack the chemical accuracy of fits that are backed by spin simulations but provide a quick model of the general lineshape of a compound How do generate a cluster to fit a region of the spectrum 1 Select the region of the spectrum that you would like to fit with a generated cluster 2 Click Generate Cluster for Region Tips and Tricks e Generated clusters have no basis in theoretical NMR They simply add a number of Lorentzian peaks that approximates the overall shape ofthe spectrum in the selected region As a result they will not allow you to accurately account for significant changes in the spectrum based on magnet frequency pH or other systematic variations e Signatures based on generated clusters will usually only 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 peak
143. led Split with a split count of 1 and click OK Use the height and frequency controls on the vertical and horizontal axes to match the first spin definition blue to the spectrum black 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 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 11 5 Tutorial Spin Simulator 116 evomx CHENOMX NMR SUITE USER MANUAL 18 19 20 21 22 23 24 25 Part Il 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
144. lp you to manage fitting and maintenance 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 in your compound library folder and return to Library Manager the updated compound is available immediately throughout Chenomx NMR Suite How do I use Send to Compound Builder LL Ul le Send to Compound Builder 1 Selecta compound in the Compound Table ae x 2 Click Send to Compound Builder Hotkey s ilh 3 Make any desired changes to the compound signature in Compound Builder 4 Savethe changes in Compound Builder 5 Close Compound Builder or close the file Tips and Tricks e Makesurethatyouhave the Date Modified column turned on in the Compound Table This allows you to 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 e Changes that you make to a compound will only be immediately visible in Chenomx NMR Suite if you save it in the compound library folder specified in the Library Manager preferences Related Topics
145. ls 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 6 3 Information Tools 32 evomx Menu Location Icon s File gt Spectrum Details l CHENOMX NMR SUITE USER MANUAL 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 are not tracked in this panel e Ifyou have just accidentally removed a layer in the Processing History you can use the Undo button to restore it Related Topics e Importing Spectra on page 16 e Processing Tools on page 34 e Convert Spectra on page 39 Spectrum Details Spectrum details describe the acquisition parameters used in acquiring 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 frequen
146. lta software package developed by JEOL In Spin Simulator parameters that modify a spin definition by splitting it to form more complex shapes Composed of a J value and a split count and include both coupled and uncoupled splits In Spin Simulator defines the magnitude ofthe split defined by a J modifier Equivalent to a coupling constant for coupled splits In Spin Simulator a graphical control used to vary the J value for the currently selected J modifier 132 evomx CHENOMX NMR SUITE USER MANUAL library Library Manager license file line broadening M magnetic equivalent ni NMRPipe NMRPipe processed spectrum data NMRPipe spectrum data no fit normalization normalized intensity 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 used to manage your Library by adding or 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 approxima
147. lution as peak shapes have changed throughout the spectrum For best results analyzing spectra using the Chenomx library choose a value that yields a total linewidth between 1 0 and 1 5 Hz The CSI definition needs adjustment following line broadening as peak shapes have changed throughout the spectrum The calculated pH is 8 37 For practice try reproducing this result using the manual tools 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 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 CHENOMX NMR SUITE USER MANUAL 21 22 23 24 25 Ap 26 27 28 29 30 Leave the Target Linewidth at its initial value of around 0 6 Hz Select the Use DSS TSP Satellites check box Click the Accept button to apply your changes to the spectrum Switch to the CSI Editor Click the Find Automatically button plying Line Broadening Switch to Line Broadening mode Enter a value of 0 4 Hz Click the Accept button to apply your changes to the spectrum Switch to the CSI Editor Click the Find Automatically button Determining the Spectrum pH 31 32 33 34 35 36 37 Switch to the pH Editor Automatic Click the Find Automatically button to
148. m compound set 94 remove from library 92 set 53 88 93 94 95 97 table 44 88 compound details author 84 ID 84 magnet frequency 84 name 84 sample concentration 84 UUID 7 84 compound library folder 2 24 remove compound from 92 rescan 92 compound set automatically update 96 delete 97 export as compound pack pack 90 new 94 panel 53 93 remove compound from 94 rename 97 smart 93 95 97 compressed SVG svgz 59 concentration 49 clear 49 export profiled concentrations 56 exported concentrations txt 29 potential 51 scale 52 set to potential 51 units 62 convert conversion settings 39 spectra 16 39 copy spectrum image to clipboard 60 coupled split 6 69 creatinine 8 11 30 CSI 8 29 editor 29 find automatically 29 internal standard 8 preserve area 29 custom color 44 46 D data acquisition 8 datdir 9 decrease vertical zoom 21 default file folder 24 layout 56 selection line 23 transform window 81 zoom 24 delete compound set 97 Delta 9 DFTMP 7 8 11 30 display options compound line 23 default selection line 23 overlay line 23 selection line 23 simulation line 23 spectrum line 23 subtraction line 23 110 sum line 23 111 DSS TSP satellites 37 E edit J modifier 69 peak 78 142 evxomx smart compound set 95 spin definition 67 transform window 81 embedded libraries 5 encapsulated PostScript eps 59 exclude region 5
149. match the overlay The Information Panel displays a warning if your overlaid spectrum 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 Overlaying a Spectrum on page 19 e Fitting Tools on page 75 e Compound Details on page 84 9 4 Information Tools 85 Chapter 10 Library Manager The Library Manager module allows you to create 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 10 1 Overview B Library Manager lest File Edit View Compounds Help Compounds a Py Chenomx 400MHz pH 4 9 Bos oes Compound Name Valid pH Range Date Added i Chenomx SO0MHz pH 4 9 Pipecolate 6 00 to 8 00 November 23 2007 eo Proline 6 00 to 8 00 November 23 2007 GE eae Propionate 6 00 to 8 00 November 23 2007 Ib Chenom etti pH 6 8 Propylene glycol 6 00 to 8 00 November 23 2007 Protocatechuate 6 00 to 8 00 November 23 2007 T Chenomx 7000 pH 4 9 Putrescine 6 00 to 8 00 November 23 2007 T Chenomx 7000 pH 6 8 Pyridoxine 6 00 to 8 00 November 23 2007 Pyroglutamate 6 00 to 8 00 November 23 2
150. 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 76 e Selecting Peaks and Clusters on page 77 e Adjusting Peaks on page 78 e Grouping Peaks as a Cluster on page 79 e Cluster Navigator on page 82 Cluster Navigator The Cluster Navigator allows you to quickly move among the clusters that you have created in the current compound signature It appears in the top left corner ofthe Spectrum View as a ordered 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 I display the clusters of a compound in the Spectrum View 1 Make sure that the Cluster Navigator is visible 2 Clicka cluster position to zoom directly to that cluster Click the left or right a
151. me Concentration mM Potential mM i Salicylate 0 0000 Salicylurate 0 0132 Sarcosine 0 1029 S Suffocysteine Q Suberate 0 0498 0 0494 Succinate 0 1094 271 compounds 3 9592 ppm 0 455 si Compound Set Panel Allows you to control which compounds appear in the Compound Table by selecting or deselecting compound sets You can create or edit compound sets using Library Manager 6 Cluster Navigator Allows you to navigate among the clusters of the currently selected compound You can enable or disable the Cluster Navigator using the View menu 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 QuickSearch Allows you to filter the Compound Table to focus on a particular compound or group of compounds 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 7 1 Overview 41 evomx CHENOMX NMR SUITE USER MANUAL 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 These tools allow you to navig
152. measured concentrations when available in Profiler Scalable vector graphics compressed with gzip compression resulting in files that are up to ten times smaller Suitable for image distribution on the internet when storage space is an issue In Spin Simulator a J modifier that links two spin definitions via a common split count and J value allowing 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 used in Processor to define the properties of the CSI for a spectrum includingthe experimental concentration in mM peak center in ppm height in si and width in Hz In Profiler the line used to indicate the currently selected compound when no custom color has been assigned to it colored blue by default In Compound Builder the limits applied to a cluster when such limits are activated but not 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 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 difluoro trimethylsilyl methyl phosphonate a pH indicator supported by Chenomx
153. mpound see Concentrations on page 49 and Transforms on page 50 If the fit does not appear reasonable reset the concentration of the compound to unknown see Concentrations on page 49 Continue with any other specific compounds you would like to investigate To identify possible compounds causing a specific peak 1 10 Select at least one Compound Set in the Compound Set Panel see Compound Set Panel on page 53 Right click on the peak and click Filter for Compounds Near x xx ppm In the Compound Table select one of the listed compounds to display the selection line and Cluster Navigator for the compound see Cluster Navigator on page 53 Set a concentration for the compound so that you can see the clusters clearly see Concentrations on page 49 Compare the shape of the selection line blue and the spectrum line black and decide whether or not it is reasonable that the selection line could be contributing to the spectrum line in the displayed region If the fit 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 fit reasonably well then proceed to determine appropriate heights and transforms for the clusters of the compound see Cluster Navigator on page 53 Concentrations on page 49 and Transforms on page 50 If the fit does not appear reasonable
154. mpounds often have additional peaks in the busier regions ofthe spectrum so fitting them first can help rule out other compounds later in the fitting process In this simple spectrum all of the compounds are quite well separated from each other and should be relatively simple to fit Basic Fit Acetate 1 Open Profiler 2 Open the sample file called Samples Profiler Basic Start cnx 3 Inthe Compound Set Panel select the compound set called Tutorial Sample Compounds which you just installed see above Zoom in on the single peak near 1 90 ppm Right click on the peak and click Filter for Compounds Near 1 91 ppm In the Compound Table select acetate No 5o Click the location of the peak 1 9 ppm in the Cluster Navigator to include the peak s full range of motion in the Spectrum View 11 3 Tutorial Profiler 102 evomx CHENOMX NMR SUITE USER MANUAL 10 11 Set acetate to its potential concentration see Potential Concentrations on page 51 for more information Click and drag the acetate signature blue to match it as closely as possible to the corresponding peak in the spectrum black You may need to zoom in more to allow more accurate adjustments You can also click and drag the controls on the horizontal and vertical axes to move the peak along only one axis at a time Clear the quick search box above the Compound Table by clicking the red X Click Show Entire Spectrum Basic Fit Pyruva
155. n 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 e Place the mouse cursor anywhere in the Spectrum View and use the mouse scroll wheel to adjust the Vertical Zoom e Middle click anywhere in the Spectrum View to apply an Auto Zoom 5 9 Spectrum View Tools 21 CHENOMX NMR SUITE USER MANUAL Spectrum Thumbnail The Spectrum Thumbnail appears in the bottom right corner of the Processor window 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 I use the Spectrum Thumbnail 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 of the solid borders of the zoom box to move that border or click and drag one of the corners to move the size and shape of the displayed region e Click anywhere in the Spec
156. n CSI adjustments and other processing steps 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 Processing History Displays a list of every processing layer that you have applied to the current spectrum and allows removal of any processing layer that you have applied using the Processor module Spectrum View Tools These tools allow you to navigate the spectrum more easily Spectrum Thumbnail Displays a thumbnail image of the current spectrum You can also use the thumbnail to navigate the spectrum at various zoom settings Q 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 1 Overview 27 Enom CHENOMX NMR SUITE USER MANUAL 6 2 Quick Reference Guide Linux Windows Mac OS X File Menu Open Ctrl O Cmd O Open Recent EJ Close Ctrl W Cmd W H Save Ctrl S Cmd S Save As EE Send to Profiler Ctrl J Cmd J Spectrum Details x ane Preferences ses Exit ee Edit Menu V Undo Ctrl Z Cmd Z fy Redo Ctrl Y Cmd Y View Menu X Scale Y Scale as lol Zoom Show Entire Spectrum Ctrl Cmd Zoom gt Set Zoom Ctrl M Cmd M h Zoom gt Undo Zoom Zoom
157. n Profiler and Compound Builder The accuracy of these settings also have a direct impact on the accuracy of profiled spectra cnx exported concentrations txt compound files xcpd and spin simulations xss The CSI editor allows you to 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 6 3 Information Tools 29 Enom CHENOMX NMR SUITE USER MANUAL How do I modify the CSI settings Menu Location View gt Edit Mode gt CSI Menu Location Tools gt Find CSI Automatically 2 Icon s P 3 4 5 1 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 Due to potential overlap with other compounds Processor cannot automatically find formate as a CSI 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 cannot find your CSI you need to use the manual tools to locate it instead Manual Click and drag
158. n existing Compound Set to focus more directly on your current project To access and edit Compound Sets you can open the Library Manager Icon s D module from Profiler Hotkey s adi Tips and Tricks Cmd L e Compound Sets that you change in Library Manager update immediately in Profiler e 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 Related Topics e Compound Set Tools on page 53 e Chapter 10 Library Manager on page 86 7 4 Compound Set Tools 55 evomx CHENOMX NMR SUITE USER MANUAL 7 5 Importing and Exporting Data You can export concentrations from your profiled spectra for further analysis bin the spectra for analysis by more traditional techniques or create images of the spectra for use in publications and presentations Export Profiled Concentrations When you have finished profiling a spectrum or set of spectra you often need the resulting concentration data in a spreadsheet or statistical analysis package Export Profiled Concentrations allows you to 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 export concentrations from one or more spectra Menu Location Icon s File Export Profiled Concentrations txt us 1 2 Start
159. n list appears in the Spin Definition Panel 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 IntheSpin Definition Panel selectthe 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 8 3 Fitting Tools 66 Enom Menu Location Icon s Simulation Remove Spin System S Menu Location Icon s Simulation Add Spin Definition e CHENOMX NMR SUITE USER MANUAL How do I remove a spin system 1 Selecta spin system from the drop down list above the Spin Definition Tabs 2 Click Remove Spin System Tips and Tricks e When you remove a spin system all spin definitions and J modifiers associated with the spin system are removed as well Related Topics e Spin Definitions on page 67 e Spin Navigator on page 68 e Spin Definition Tab on page 69 e Simulation Details on page 71 Spin Definitions Spin Simulator creates computer models of the interactions among the members of a spin system Within Spin Simulator a member of a spin system may be considered equivalent to a single proton or a group of protons that are both chemical shift equivalent and magnetic equivalent These members of spin systems are described by spin definitions and are the
160. n specify a series of spectrum files or one or more folders containing spectrum files as the source 3 Chooseabinning method to apply to the specified spectra You can use a defined number of bins or a defined bin size in ppm across a range ofthe spectrum in ppm or create one bin per frequency domain data point full resolution binning You can also use bins based on the transform windows of compounds in a selected Compound Set targeted binning 4 Choose a binning target You can bin spectra based on the sum line standard binning or the subtraction line residual binning 5 Choose regions ofthe spectrum to exclude from binning if desired You can specify any regions ofthe spectrum using start and end values in ppm 6 Chooseanormalization 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 7 Choose output options for the binning results You can label bins based on their mid points their start points or the range covered by each bin Also you can have bins ordered from high to low frequency 10 0 to 0 0 ppm or low to high frequency 0 0 to 10 0 ppm Finally you can choose to use the full path in file labels rather than just the file name Tips and Tricks e Binning can take a long time especially on older computers or particularly large datasets If you have never tried binning be
161. n 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 same 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 Processing Advanced 1 Reference Deconvolution I Icon s aD 3 Ctrl Alt 4 Hotkey s 3 Cmd Alt 4 f In the CSI editor fit the red CSI peak to your spectrum See CSI Editor on page 29 for details Menu Location Switch to Reference Deconvolution mode Zoom in to 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
162. n the same spin system e When you remove a coupled J modifier you will remove it from both spin definitions to which it applied If you only want to remove the J modifier from one spin definition you will have to uncouple it first e Uncoupling a coupled J modifier will result in an uncoupled split on each of the two 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 particular J modifier in the Spin Definition Tab Related Topics e Spin Systems on page 66 e Spin Definitions on page 67 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 oftransitions present in the current simulation Tips and Tricks e When you do not have a spectrum overlaid 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 overlaid spectrum Related Topics e Overlaying a Spectrum on page 19 e Spin Systems on page 66 e Spin Definitions on page 67 8 3 Fitting Tools 71 Chapter 9 Compound Builder You can only use Compound
163. n the simulation and exponentially with the number of distinct J couplings Spin Simulator monitors the overall complexity ofyour simulation as you work and if you attempt to take an action that would result in unusable simulation times the action will be cancelled and you will see a warning dialog indicating that the resulting simulation would be too Menu Location Icon s Hotkey s complex New Simulation New Simulation creates a new simulation file xss The new simulation file has the default File New Simulation simulation frequency of 800 MHz P Tips and Tricks Ctrl N e The new simulation file does not have an overlaid spectrum You should overlay a Cmd N spectrum before you continue creating a simulation You need to save the new file in order to retain changes that you have made Related Topics e Overlaying a Spectrum on page 19 e Simulation Details on page 71 Spin Systems If you need to model many protons with 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 How do add a new spin system Menu Location Icon s Simulation Add Spin System 1 Click Add Spin System 2 fthisis the first spin system you are adding a new dropdow
164. ne 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 fits of the spectra in your dataset Test Mixtures As you fit a series of spectra in a larger dataset you will notice that the fit of some mixtures of compounds is difficultto determine You may wantto try running controlled test mixtures ofthe compounds in question to establish their behaviour under your experimental conditions and use information from the test mixtures to guide your fits ofthe larger dataset Test mixtures will help increase confidence and consistency in your fitting results 11 4 Tutorial Targeted Profiling 109 CHENOMX NMR SUITE USER MANUAL Fitting Clusters Once you have selected a compound to fit you need to fit the individual clusters of the compound to their respective regions ofthe spectrum There are several common approaches to fitting clusters and in a typical spectrum more than one method will be necessary You should try to maintain a consistent approach to fitting spectra in a dataset as this will help you obtain accurate and consistent results from your analysis Basic Fits Compound Line The simplest fit for a cluster is to adjust the cluster so that the compound line blue by default unless you have assigned custom colors matches the spectrum line black This
165. ng a series of compounds to an experimental spectrum Practically targeted profiling includes the two tasks ofidentifying a compound or compounds that you would like to fit and fitting the individual clusters of each compound to their respective regions of the spectrum Identifying a compound to fit 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 fitting 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 Fitting individual clusters in a region ofthe spectrum requires some care and attention the most important facet of any fitting technique is applying it consistently to all spectra in a dataset Fitting 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 of these methods are described below you may discover other methods as you analyze more spectra 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 literatu
166. ng of your spectrum before proceeding with baseline correction Most spectra require some degree of baseline correction particularly if you need accurate quantification in Profiler You should 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 Otherwise you can apply automatic or manual baseline correction after you have imported the spectrum In either case a Baseline Correction layer appears in the Processing History panel you can remove this layer if necessary 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 apply baseline correction to my spectrum Menu Location Processing gt Baseline Correction 1 Switch to Baseline Correction mode Teee 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 6 4 Processing Tools 35 evomx CHENOMX NMR SUITE USER MANUAL Manual Click on the spect
167. nger requires fully assigning a compound and deciphering all of its coupling relationships before you start creating a new compound You can create approximate compound signatures starting with Compound Builder but creating signatures that will be useful in analyzing more than a narrow range of spectrum conditions will require creating a simulation in Spin Simulator first You can save compound signatures that you generate using Compound Builder as compound files xcpd Compound files can be added directly to your library either by saving or copying them directly to your library folder or importing them through Library Manager see Compound Library Folder on page 4 for more details 2 4 Compound Library Folder Earlier releases of Chenomx NMR Suite revolved around multiple compound libraries For example you might have a pair of Chenomx compound libraries at 800 MHz One for pH 6 8 and one for pH 4 9 In addition you could have any number of custom libraries that you 2 1 Signature Builder 4 evomx CHENOMX NMR SUITE USER MANUAL had created which could include compounds from Chenomx libraries as well as compounds that you had created yourself As a result you could easily end up with multiple copies of a compound in different libraries and you could not necessarily tell whether you were using an up to date copy of the compound or an old or just different copy In Chenomx NMR Suite 5 0 you have only one library which is
168. nsider In the Compound Table select 2 oxoglutarate and set it to its potential concentration Adjust the 2 oxoglutarate cluster near 2 43 ppm to best fit the spectrum Notice that the sum line red at 2 417 ppm now fits the spectrum more closely than it did with only pantothenate adjusted Since 2 oxoglutarate is quite simple you can finish fitting it before continuing with pantothenate Click the location of the remaining 2 oxoglutarate cluster 3 0 ppm in the Cluster Navigator and adjust the cluster there to best fit the spectrum Use the frequency control to prevent further changes to the concentration Select pantothenate again 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 Click the location of the next pantothenate cluster 3 4 ppm in the Cluster Navigator and adjust the cluster at 3 39 ppm using the frequency control In the Compound Table set fucose and taurine each to their potential concentration and then select taurine Use the Cluster Navigator to display the taurine cluster near 3 3 ppm and adjust it to fit the spectrum Setting the concentration for taurine here will make it easier to fit the other cluster near 3 4 ppm Return to the taurine cluster near 3 4 ppm and use the frequency control to match it to the spectrum In overlapped regions like this the sum line red becomes a better in
169. o 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 2 Type your search terms in the Quick Search box at the top left of the Compound Table The contents ofthe Compound Table updates to show all compounds matching your current entry 3 Click the clear button at the right edge of the search box to cancel the search and restore the full list of compounds This 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 88 e Show Archived Compounds on page 91 e Remove Selected Compounds from Library on page 92 e Compound Set Tools on page 93 Import 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 Import Compounds helps you consolidate these sources collecting the embedded compound signatures for use in Profiler How do I import compounds into my library Menu Location Icon s Hotkey s Compounds Import Ctrl I Cmd l 1 OpentheImport Compounds wizard 2 Select any combination of compound files xcpd compound packs p
170. odifiers represented in the simulation Spin Navigator Allows you to 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 These tools allow you to navigate the spectrum more easily 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 X Scale and View gt Y Scale settings Also displays information about recent user actions 8 2 Quick Reference Guide o eo Linux Windows Mac OS X File Menu 9 New Simulation Ctrl N Cmd N Open Ctrl O Cmd O Open Recent EJ Close Ctrl W Cmd W tH Save Ctrl S Cmd S Save As e ERE Preferences Exit o bs Edit Menu V Undo Ctrl Z Cmd Z C5 Redo Ctrl Y Cmd Y Select All Spin Definitions Ctrl A Cmd A View Menu X Scale mt Y Scale el Zoom Show Entire Spectrum Ctrl Cmd a Zoom Set Zoom Ctrl M Cmd M w Zoom gt Undo Zoom E Zoom Redo Zoom y Zoom Auto Zoom Ctrl F Cmd F 8 2 Quick Reference Guide 64 Enom CHENOMX NMR SUITE USER MANUAL ys Zoom gt Increase Vertical Zoom Zoom gt Decrease Vertical Zoom Show Spin Navigator Ctrl Shift N Cmd Shift N Show J Value Editor Ctrl Shift J Cmd Shift J Show Overlay
171. of Chenomx 8 1 Overview NMR Suite or if you are using a time limited trial version of Chenomx NMR Suite uos Puno CN NN TUE File Edit View Simulation Help meg ov ga o 1 El IE all Ls i Spin Definition 0 Spin Definitions 41 34 33 23 21 20 20 Protons 1 Center ppm 1 97865 gt SD2 gt 7 57 Hz Width sw 1 282 J Modifiers Qy cowedtos 1 13 23 Hz a 0SD2 1x Coupl coupledto sos 1 6 65 Hz coupled to sos 1 7 44 Hz coupled to sos 1 x 7 4042 Simulation Details Frequency MHz 799 81 Number of Spin Systems Number of Transitions 116 of 116 possible Number of Modfiers amp 13 o SpinDefinition Panel Displays the Spin Definition Tab for the currently selected spin definition including its center number of protons represented and width Also allows you to select other spin systems via a drop down menu and spin definitions via the tabs J Value Editor Allows you to vary the J value for the currently selected J modifier J Modifier List Allows you to add select edit or remove J modifiers associated with the currently selected spin definition e d 8 1 Overview 63 Enom CHENOMX NMR SUITE USER MANUAL Simulation Details Display information about the current simulation including the simulation frequency and numbers of spin systems transitions and J m
172. of acompound to Compound Builder for editing by clicking File gt Send to Compound Builder or by double clicking on the compound Quick Search Allows you to filter the Compound Table to focus on a particular compound or group of compounds Status Bar Displays information about recent user actions 10 1 Overview 86 CHENOMX NMR SUITE USER MANUAL Enom 10 2 Quick Reference Guide Linux Windows Mac OS X File Menu D New Compound Set Ctrl N Cmd N A New Smart Compound Set Ctrl Shift N Cmd Shift N 4 Update Compound Versions Ctrl U Cmd U ig Edit Smart Compound Set Ctrl E Cmd E D Rename Compound Set Ctrl R Cmd R IF Delete Compound Set T A Send to Compound Builder Ctrl J Cmd J Preferences Exit Edit Menu V Undo Ctrl Z Cmd Z C Redo Ctrl Y Cmd Y View Menu Show Archived Compounds iss HY Change Columns ee Compounds Menu Add Selected Compounds to i anal eee Compounds from gt Delete ae a joi Selected Compounds from Ctrl Delete Cmd Delete Import aus Ta Rescan Compound Library A Help Menu d Contents F1 F1 Q Search E td Save Application Log exe E Activation Details aes 10 2 Quick Reference Guide 87 CHENOMX NMR SUITE USER MANUAL 9 About Chenomx NMR Suite Ses 10 3 Library Tools Library Manager allows you to browse and manage the contents of your
173. ompound Add Peak utum Ctrl K Cmd K 1 Switch to Add Peak mode The mouse cursor changes to a large crosshair 2 Clicksomewhereonthe spectrum to add anew peak The point that you click defines both the position and the height of the new peak Tips and Tricks e 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 Thenew peak appears in the peaklistin numerical order with the currently displayed peaks not necessarily at the beginning or end of the list e 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 e 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 e 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 Related Topics e Selecting Peaks and Clusters on page 77 e Remove Selected Peaks on page 78 e Adjusting Peaks on page 78 e Grouping Peaks as a Cluster on page 79 e Optimize Selected Peak Shapes on page 79 9 3 Fitting Tools 76
174. ompound Builder 11 2 Tutorial Processor 101 evomx CHENOMX NMR SUITE USER MANUAL 11 3 Tutorial 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 ina 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 A custom compound pack has been included with the sample files to provide you with the same compound signature that were used to prepare the tutorial You need to install the compound pack before you continue with this tutorial Install the custom compound pack 1 Open Library Manager Click Compounds gt Import Click the Browse button In the Samples Library Manager folder select Sample pack Click Choose Files Click Next Click Finish o on oO gl m D P Verify that a compound set called Tutorial Sample Compounds now appears in the Compound Set Panel Part Basic Profiling Techniques Frequently the simplest way to start analyzing a spectrum is to fit compounds that are easily identifiable first These co
175. on mode Click the Auto Linear button to have Processor locate the spectrum endpoints automatically Automatic Click the Auto Spline button to have Processor place a set of breakpoints on the spectrum for you Manual Click in the spectrum viewing pane to add breakpoints for a cubic spline baseline fit Use more points where the baseline is strongly curved and fewer points where it is basically linear 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 18 Switch to the CSI Editor Zoom in on the single 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 Automatic Click the Find Automatically button to have Processor attemptto match the peak automatically Manual Use the Adjustment Handle and width controls to adjust the shape of the red overlaid peak to match the black spectrum line as closely as possible Click the Show Entire Spectrum button to restore a view of the whole spectrum Applying Reference Deconvolution 19 20 Zoom in on the DSS peak at 0 ppm Switch to Reference Deconvolution mode 11 2 Tutorial Processor 100 Enom The CSI definition needs adjustment following reference deconvo
176. on page 24 e Profiling Tools on page 44 Spectrum Details Spectrum Details allows you to view basic properties of the current spectrum including sweep width magnet frequency pulse sequence and so on as well as user defined properties such as sample pH and comments that have been added in Processor Tips and Tricks e All of 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 6 Processor on page 27 7 6 Information Tools 61 evomx CHENOMX NMR SUITE USER MANUAL Concentration Units You can change the units of concentration used in the Compound Table Available units Menu Location View gt Concentration Units include millimoles per litre mM micromoles per litre uM and milligrams per decilitre mg dL Tips and Tricks The concentration units setting affects both how concentrations appear in the Compound Table and how they are exported You should ensure that the concentration units are set appropriately before you export concentrations The maximum allowed concentration for any compound is 5000 mM 5 M When you have selected mg dL as the concentration units 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 Concentrations in mg dL are only available for
177. on page 50 e Potential Concentrations on page 51 e Scale Concentrations on page 52 e Compound Set Tools on page 53 e Export Profiled Concentrations on page 56 Reference Panel on page 61 e Concentration Units on page 62 Transforms The frequencies of clusters in a compound signature that you are using may be different from those in the actual spectrum Such differences can occur due to changes in solution pH ion concentrations and other matrix effects Transforms allow you to move the clusters from their starting locations to compensate for these effects and better fit the spectrum Transforms are 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 How do I set transforms 1 Selecta 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 2 Clickanddragthe blue triangle for a cluster along the horizontal 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 7 3 Profiling Tools 50 evomx CHENOMX NMR SUITE USER MANUAL 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 t
178. one ofthe the methine signals 4 11 5 Tutorial Spin Simulator 115 evomx CHENOMX NMR SUITE USER MANUAL 10 11 12 13 14 15 16 17 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 Open Spin Simulator Overlay the valine spectrum called Samples Spin Simulator Valine cnx Add spin definitions for each of the signals from the assignment above starting from the right hand side of the spectrum low numbers and moving left to higher numbers You now have SD0 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 Spin Definition Panel at the far left edge of the Spin Simulator window Zoom in to 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 Measure the 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 Select SD0 0 978 ppm by clicking on it in the graph or clicking on its tab in the Spin Definition Panel Right click on SDO blue and click Add J Modifier Enter a J value of 7 02 Hz select Uncoup
179. ool of compound files stored in a folder designated via Library Manager preferences 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 Chenomx file format pack designed to store a collection of compound files xcpd for exchange among users of Chenomx NMR Suite 129 evomx CHENOMX NMR SUITE USER MANUAL compound set Compound Set Panel Compound Table compressed scalable vector graphics coupled split creatinine CSI CSI editor default selection line default transform window Delta DFTMP DSS List of compounds defined in Library Manager that appears in Profiler for use during profiling Can refer to any set appearing in the Compound Set Panel in Profiler or to fixed lists of compounds specifically as opposed to the automatically updating lists known as smart compound sets List of available compound sets appearing in Profiler based on the current compound library Allows modifying 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 potential and
180. orted 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 ina spreadsheet program or if you prefer the transposed layout If you intend to open the exported file in Microsoft Excel 2003 or earlier you should limitthe 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 44 7 5 Importing and Exporting Data 56 evomx Menu Location Icon s File gt Export gt Profiled Compounds pack CHENOMX NMR SUITE USER MANUAL e Compound Set Tools on page 53 e Concentration Units on page 62 Export Profiled Compounds When you are collaborating with other people on a project you may have different versions of 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 Compound packs may be exchanged with other users of Chenomx NMR Suite and imported via Library Manager into a new compound set You can then be certain that you and your collaborator are always fitting spectra for that project using the
181. ound 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 11 7 Tutorial Library Manager 127 Glossary 1r A acquisition time activation animated zooming application log archived compounds auto baseline correction auto phasing auto zoom baseline correction basic fit 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 Smooth transitions between zoom settings in the Spectrum View of Processor Profiler Compound Builder or Spin Simulator Text file generated by Chenomx NMR Suite for troubleshooting purposes Old versions of a compounds currently present in your Library Only visible in Library Manager when Show Archived Compounds is turned on 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 Profil
182. ounds 54 UUID 7 84 V valine 115 121 126 Varian processed data phasefile 9 16 spectrum file fid 16 VNMR 9 VNMRj 9 W water deletion 38 suppression 112 wings 35 X XWIN NMR 9 Z zero order phase 34 zoom animated 24 auto 21 box 21 22 decrease vertical 21 default 24 increase vertical 21 redo 21 set 20 show entire spectrum 20 undo 21 145
183. oup uncoupled 69 J value 6 69 J value editor 69 JCAMP DX spectrum file jdx 16 JEOL Delta spectrum file jdf 16 L license file cnxlic 1 line broadening 36 line color 24 M magnet frequency 84 N new compound 75 compound set 94 simulation 66 smart compound set 95 NMR parameters acquisition time 9 relaxation delay 9 spectral width 9 temperature 9 NMRPipe processed data ft2 16 spectrum file fid 16 no fit 114 normalization 58 0 optimize selected peak shapes 79 output options 58 overlay line 23 overlay spectrum 19 P peak add 76 edit 78 group as cluster 79 list 85 optimize selected 79 remove 78 select 77 pH editor 30 find automatically 30 indicator 8 internal standard 8 spectrum 30 pH indicator creatinine 8 11 30 DFTMP 7 8 11 30 imidazole 8 11 30 phasing 34 automatic 34 first order phase 34 zero order phase 34 portable document format pdf 59 portable network graphic png 59 PostScript ps 59 potential concentration 51 preprocessing 32 34 ACD Labs 9 Bruker processed data 1r 16 Delta 9 JCAMP DX spectrum file jdx 16 JEOL Delta spectrum file jdf 16 NMRPipe processed data ft2 16 Varian processed data phasefile 9 16 VNMR 9 VNMRj 9 XWIN NMR 9 preserve CSI area 29 processing 143 Enom baseline correction 35 history 32 line broadening 36 phasing 34 preprocessing 32 34 referenc
184. ow do edit a Smart Compound Set File gt Edit Smart Compound Select a Smart Compound Set in the Compound Set Panel Click Edit Smart Compound Set Make any desired changes to the name of the set magnet frequency restriction or filters Click OK Tips and Tricks 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 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 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 Library Tools on page 88 Compound Set Panel on page 93 Compound Sets on page 94 Rename Compound Sets on page 97 Delete Compound Sets on page 97 Update Compound Versions When you create a compound set the compound signatures included in the set are based on the contents of your library at the moment you create the set If you create new updated versions of compounds in that set using Compound
185. page 76 e Selecting Peaks and Clusters on page 77 e Adjusting Peaks on page 78 e Transform Windows on page 81 e Cluster Navigator on page 82 Optimize Selected Peak Shapes Adding peaks to a signature and adjusting them to approximately model a particular region of the spectrum is fairly simple However the task of fine tuning those peaks to accurately fit the lineshape in that region can be tedious Once you have approximated the fit of a region ofthe spectrum you can use Compound Builder s optimization algorithms to rapidly obtain a more refined fit of the region 9 3 Fitting Tools 79 Enom Menu Location Icon s Hotkey s Tools Optimize Selected Peak Shapes amp ES Ctrl I Cmd l Menu Location Icon s Hotkey s Tools Generate Cluster for Region an Ctrl Shift I Cmd Shift I CHENOMX NMR SUITE USER MANUAL How do optimize the fit of peaks in my compound signature 1 Select the 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 fit is reasonably close to the actual shape of the spectrum Simulating the compound in Spin Simulator can often give you a very good starting fit Related Topics e Add Peak on page 76 e Selecting Peaks and Clusters on page 77 Ad
186. plex spectrum The best method for learning many of the techniques that you can use to fit such a spectrum is probably practice fitting progressively more complex spectra until you develop a level of proficiency More detailed discussions of profiling strategies are available elsewhere in this manual see Tutorial Targeted Profiling on page 108 Fitting a Spectrum on page 12 and Fitting Overlapped Regions in a Spectrum on page 14 11 3 Tutorial Profiler 104 Enom CHENOMX NMR SUITE USER MANUAL Getting Started 1 2 3 Open Profiler Open the file called Samples Profiler Advanced Start cnx Select the Tutorial Sample Compounds set in the Compound Set Table Although completely non overlapping compounds are easy to fit they cannot give any further insight into the fit of other compounds in the spectrum You should generally profile these compounds first so that you can focus on the more challenging regions ofthe spectrum Since we covered the relevant techniques in Part I they will not be covered in detail here Fitting Compounds with No Overlap 4 Usingthe basic techniques discussed in Part I fit the following twelve compounds e 3 Indoxylsulfate 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 the non overlapped compounds have been fit a more systematic approa
187. pound Line Color Simulation Line Color Subtraction Line Color CSI Line Color Changes the color of the background in the Spectrum View Changes the color of the spectrum line in the Spectrum View in Processor and Profiler The default color is black Changes the color of the spectrum overlay line in the Spectrum View in Compound Builder and Spin Simulator The default color is black Changes the color of the sum line in the Spectrum View in Profiler The default color is red Changes the color of the compound line in the Spectrum View in Compound Builder The default color is red Changes the color of the simulation line in the Spectrum View in Spin Simulator The default color is red Changes the color ofthe subtraction line in the Spectrum View The default color is green Changes the color of the CSI in the CSI Editor Spectrum View in Processor The default color is red 5 11 Preferences 25 CHENOMX NMR SUITE USER MANUAL Zoom Box Color Selection Line Color Default Zoom ppm Changes the color of the selected area in the Spectrum View and the Spectrum Thumbnail The default color is red Changes the color of the selection line in the Spectrum View in Profiler Compound Builder and Spin Simulator The default color is blue Sets the frequency range of the Spectrum View that initially appears when you open a file File Preferences Display Recent Files Default File Folder
188. pound set You can then be certain that you and your collaborator are always fitting spectra for that project using the same collection of compound signatures How do export a compound set to a Compound Pack Menu Location Icon s Compounds Export as Compound Pack 1 2 7 3 Open the Export as Compound Pack dialog Select the compound set that you would like to export Enter a name for the exported compound pack This name is used to label the associated compound set when the compound pack is imported into anotherlibrary 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 This 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 e You and your collaborator each need a valid licensed copy of Chenomx NMR Suite installed in order to make use of compound packs If you only want to export compounds that are actually fit in a particular spectrum load the spectrum in Profiler and use Export Profiled Compounds Related Topics Import Compounds on page 89 Compound Set Panel on page 93 Compound Sets on page 94 10 3 Library Tools 90 CHENOMX NMR SUITE USER MANUAL e Smart Compound Sets on page 95 Send to Compound Builder Library Manager can he
189. ps and Tricks Hotkey s Cmd Shift K e A Compound Set called Profiled Compounds always appears at the top of the Compound Set Panel This set includes all compounds in the current spectrum that 7 4 Compound Set Tools 53 evomx Menu Location Icon s Hotkey s Compounds Selected Compound Update Version D Ctrl U Cmd U CHENOMX NMR SUITE USER MANUAL have been modified based on concentrations transforms custom colors highlights 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 This includes modifying selection rules for Smart Compound Sets manually changing Compound Sets by adding or removing compounds and creating or deleting Compound Sets Related Topics Profiling Tools on page 44 Update Profiled Version One Compound on page 54 Update Profiled Versions Several Compounds on page 54 Open Library Manager on page 55 Update Profiled Version One Compound You can easily make changes to compounds in your library add new compounds or remove outdated ones using Compound Builder and Library Manager You will encounter spectra that you profiled with different versions of th
190. quick test of each alternative indicates that the former option yields a better approximation of the spectrum 29 Adda J 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 Usethe J Value Editor to fine tunethe modifier coupling SDO to SD1 The resulting value is 13 23 Hz 34 Use the frequency width and height controls to match SD1 and SDO as closely as possible to the spectrum line 35 Save the simulation file If you would like to review the sample simulation of proline you should not replace the file called Samples Spin Simulator Proline xss 11 6 Tutorial Compound Builder Introduction You can use the Compound Builder module to create compound signatures that you can add to your library Although you can create compound signature from scratch directly in Compound Builder you can model complex compounds more accurately if you simulate them in Spin Simulator first The simulation gives you a good starting point from which to prepare a high quality compound signature Part Simple Compound In order to become familiar with the various tools available in Compound Build
191. r 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 allows a good fit ofthe 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 Usethe frequency width and height controls to match SD3 as closely as possible to the spectrum line 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 24 Adda 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 lar
192. ra PER credi Dee A 93 Compound Sets seisin ns tini deccxa c xu cR pe piRAIU a R RAA 94 Smart Compound Sets e E READ eed eee 95 Update Compound Versions eesesseseeeem mmm 96 Rename Compound Sets er repite HEX ERRUE NAE S E ME XI NM DR Ea 97 Delete Compound Sets erri toti inei i ia eni 43 times caeatenens 97 CHENOMX NMR SUITE USER MANUAL V1 TWO rial e 99 114 File Location Note erret eR e a oe EX LEY SERRE TUR FEA EE np eae 99 11 2 Tutorial ProCeSsOP eicit tir na Een tarnen na a Ex red enar ao ERE Eae unu as 99 Introduction eoe re a ERR TE x FEXFERe e Era a aia 99 Processing d SpectrUm iueseecsseseecesaesessetaee enna samnaddade cadecdecwad iaia 99 11 3 Tutorial Promler scii eiesceer xe rer tre ape Eee aaa 102 liisgestitent rge e 102 Part I Basic Profiling Techniques seseee 102 Part II Advanced Profiling Techniques 0c scceceeeneeeeeeeeeeeaeeeeeeeees 104 11 4 Tutorial Targeted Profiling eseeeeeeenm me 108 Identifying Compounds 5 12 tat nanaii a ueste RE EEEE 108 yissipACidcit E 110 11 5 Tutorial Spin Simulator cessisse cea ecdseteeenseeeneecdeneeeees 115 INtrO MUCtION e EET 115 Part I Simple Simulation sssssseeenn mmm 115 Part II Complex Simulation eeseseseseeeenemne 117 11 6 Tutorial Compound Build
193. rder to analyze a spectrum with Chenomx NMR Suite you must first process your 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 e ACD Labs software package Export your spectra to the JCAMP DX format jdx files To ensure maximum compatibility with the Chenomx Metabolite Library you should zero fill your data and process all spectra using an appropriate combination of reference deconvolution and line broadening to yield a maximum linewidth of 1 0 to 1 3 Hz When zero filling you should 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 When you import spectra using Processor you can do this by selecting the Automatic option for zero filling You should not apply any other transform to the data such as sine bell or Gaussian functions For the best results in analyzing your spectra with Chenomx NMR Suite you must properly phase and baseline correct all of your spectra 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 are avail
194. rdized area standardized intensity standardized width starred compound subtraction line subtraction line fit 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 anda 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 NMR Suite used to 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 Acurved 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 the split count may be
195. re 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 filter the Compound Table to include only compounds that can appear at a certain frequency or in a certain range of frequencies Right click on the spectrum and click Filter 11 4 Tutorial Targeted Profiling 108 evomx CHENOMX NMR SUITE USER MANUAL for Compounds Near x xx ppm to select a single frequency Alternately select a region by double clicking on the spectrum and click dragging across a range 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 As a result the number of compounds displayed using the frequency filters varies with your library selection For example the pH 4 9 version of a given compound set e g at 800 MHz displays more compounds than the pH 6 8 version of the same compound s
196. return the concentration of the compound to unknown see Concentrations on page 49 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 48 If none of the compounds in the list of potential candidates provides a reasonable fit near the peak that you are investigating you should consider the possibility that the compound causing the peaks is not in your compound library To identify all compounds contributing to a particular region 1 Select at least one Compound Set in the Compound Set Panel see Compound Set Panel on page 53 Select a region in the Spectrum View see Select Region on page 22 Right click inside the selected region highlighted in grey and click Filter for Compounds in Selected Region In the Compound Table select one of the listed compounds 4 3 Identifying Compounds 13 evomx CHENOMX NMR SUITE USER MANUAL 5 Seta concentration for the compound so that you can see the clusters clearly see Concentrations on page 49 6 Comparethe shape ofthe selection line blue and the spectrum line black and decide whether or not it is reasonable that the selection line could be contributing to the spectrum line in the displayed region 7 Ifthe fit appears reasonable in the region near the peak that you are invest
197. ributing to the sum line at the frequency that you clicked e 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 e You can perform frequency and frequency range searches directly from the Quick Search box For example 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 7 3 Profiling Tools 48 evomx CHENOMX NMR SUITE USER MANUAL Related Topics e Spectrum View Tools on page 20 Preferences on page 24 e Compound Table on page 44 e Compound Set Tools on page 53 Concentrations While profiling a spectrum you measure compound concentrations by determining heights of compounds signatures that best fit peak heights in the current spectrum You can only adjust the concentration of a compound that you have 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 ofall other peaks and clusters corresponding to the compound scale proportionately When you have set a compound concentration to 0 00 mM or greater Profiler adds it to the Profiled Compounds set at the top of the Compo
198. rrow to move sequentially through the list of clusters 9 3 Fitting Tools 82 e CHENOMX NMR SUITE USER MANUAL ENOMX Tips and Tricks e Click on a cluster and drag along the Cluster Navigator to include adjacent clusters in the Spectrum View Related Topics e Add Peak on page 76 e Selecting Peaks and Clusters on page 77 e Adjusting Peaks on page 78 e Grouping Peaks as a Cluster on page 79 e Transform Windows on page 81 9 4 Information Tools While creating compound signatures you can access extended information about compounds known to Chenomx view and update details associated with the current compound and more precisely manage peaks and clusters in complex compounds Reference Panel The Reference Panel displays information specific to the compound match the Chenomx ENUEEEUSUES View gt Show Reference Panel Compound ID that you have specified in the Compound Details This includes a structure image molecular formula and weight alternate names and links to external reference sites fe eo You can use this information to better understand the structure and behaviour of the Ctrl R compound as you prepare its signature Hotkey s nda 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 of th
199. rtable network graphics PostScript potential concentration preprocessing In Compound Builder an operation that automatically adjusts the centers heights and widths of the selected peaks to fit the overlaid spectrum based on minimizing the average intensity of the subtraction line 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 peaks positions of one or more pH indicators Compound added to a sample to allow determination of 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 packages 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 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
200. rum has a baseline that describes a smooth curve across the entire width of the spectrum e In spectra of aqueous samples the water peak may be distorted relative to the rest ofthe spectrum do not use the water peakto determine phasing Instead try to obtain smooth baseline curves to either side of the water peak e You should usually adjust the zero order phase angle more than the first order phase angle but remember that the requirements of a specific spectrum may vary 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 Importing Spectra on page 16 e Processing History on page 32 e Baseline Correction on page 35 e Reference Deconvolution on page 37 e Convert Spectra on page 39 Baseline Correction Baseline correction allows you to 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 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 you should check the phasi
201. rum 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 2 Baseline Correction 2 point linear or cubic splines You should not apply reference 3 Reference Deconvolution deconvolution to a spectrum that is poorly phased or has a 4 Line Broadening 0 to 1000 Hz if necessary poor baseline 5 Water Deletion Processing a Spectrum Getting Started 1 Open Processor All files mentioned in this 2 Open the spectrum Sample fid fid tutorial are in the folder specified at the beginning of the 3 Inthe Import Varian Raw FID Dialog tutorial e Select DSS as the Chemical Shape Indicator and set its concentration to 0 484 When you import your own mM spectra use a CSI concentration appropriate to your samples e Expand the Advanced Details section 11 1 File Location Note 99 Enom A warning appears stating that Processor could not determine the pH automatically Click the OK button to pro
202. rum 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 Click the Accept button to apply your changes or click the Cancel button to discard them Tips and Tricks Even if you intend to manually adjust baseline correction you may find it helpful to use the Auto Linear function first Auto Linear allows Processor to first locate the natural endpoints of the spectrum giving you a useful starting point for any more complex baseline fit When setting breakpoints you should 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 Importing Spectra on page 16 Processing History on page 32 Phasing on page 34 Reference Deconvolution on page 37 Convert Spectra on page 39 Line Broadening Line broadening is a mathematical operation that multiplies your fid by an exponential function before the fid is Fourier transformed This effectively increases the linewidth in your spectrum while averaging out instrument noise You may not need to apply line broadening to ever
203. ry If you are certain that you no longer want a compound accessible in Chenomx NMR Suite you can remove it from your library This operation physically removes the compound from your computer s file system Do not confuse this with removing a compound from a Compound Set How do I remove compounds from my library Menu Location panned eue ted 1 Selectthe compound that you would like to remove in the Compund Table ompounds from Library Joni x 2 Click Remove Selected Compounds from gt Library MEUS Ctrl Shift Delete Tips and Tricks Cmd Shift Delete e When you have removed compounds from the library you cannot recover them through Undo On systems with an active Recycle Bin or Trash folder you may be able to recover the deleted files via your operating system s restore function Related Topics e Compound Table on page 88 e Quick Searches on page 89 e Show Archived Compounds on page 91 e Rescan Compound Library on page 92 e Compound Set Tools on page 93 Rescan Compound Library If you have made changes to your Compounds folder specified in the Library Manager Menu Location ComPounds gt Rescan Compound Preferences directly through your operating system s file manager the changes normally Library are visible only when you next run Chenomx NMR Suite after shutting down all modules conis Ta You can rescan the library on demand to make the changes visible without reloading a module Tips an
204. s and Tricks e You must have a spectrum simulation or compound currently displayed in order to use the tape measure e The tape measure remains in the Spectrum View until you change the current view by scrolling zooming or selecting a new region using the Select Region tool 5 10 Display Options There are a number of ways in which you can customize modules in Chenomx NMR Suite to display information as you would like to see it You can toggle the display of graph elements in the Spectrum View and you can change scales You can find all of the following options in the View menu Table 5 2 View Menu Options X Scale Changes the units represented on the horizontal scale in the Spectrum View Available units are ppm and Hz Y Scale Changes the units represented on the vertical scale in the Spectrum View Available units are si standardized intensity and ni normalized intensity Show Spectrum Line Toggles the display ofthe spectrum line in Processor and Profiler The spectrum line represents data from the reference spectrum and appears black by default Show Overlay Line Toggles the display of the overlay line in Compound Builder and Spin Simulator The overlay line represents data from the reference spectrum that you can use to build a compound or simulation and appears black by default Show Subtraction Line Toggles the display ofthe subtraction line in Profiler Compound Builder and Spin Simulator The subtraction line r
205. s in the Preferences Related Topics Preferences on page 24 Set Zoom Menu Location View Zoom Set Zoom You can set the Spectrum View to display specific frequency horizontal and height vertical fanis rey ranges Displaying specific ranges can be useful for preparing illustrations or focusing ona Ctrl M particular area of the spectrum Hotkey s iioii How do I zoom to specific frequency and height ranges 1 Openthe 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 Enterthe 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 remain intact 5 9 Spectrum View Tools 20 CHENOMX NMR SUITE USER MANUAL Undo Redo Zoom MENLO CHON View gt Zoom gt Undo Redo Zoom Just as Undo and Redo allow you to recall recent actions Undo Zoom and Redo Zoom allow iee A you to recall recent views of the spectrum Hotkey s or Tips and Tricks e You can access up to 20 recent views through Undo Zoom e Redo Zoom is not available until you have used Undo Zoom at least once Au
206. s or registered 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 Solaris Java and JavaHelp are trademarks of Sun Microsystems Inc in the United States and other countries Copyright 1992 2008 Sun Microsystems Inc Linux is a registered trademark of Linus Torvalds Other brand and product names are trademarks or registered trademarks of their representative holders and should be noted as such viii Chapter 1 Introduction Welcome to Chenomx NMR Suite This manual will help you to use Chenomx NMR Suite software to process and profile NMR spectroscopic data Before you begin analyzing samples with Chenomx NMR Suite you need to install and activate the software Also accurate analysis of your NMR spectra with Chenomx NMR Suite requires good sample preparation and the acquisition of high quality spectra 1 1 Installation Chenomx NMR Suite requires a Java Runtime Environment Please download and install the latest version of Java from Sun Microsystems http java com After installing the software you need to activate it Please see Activation and Licensing on page 1 for more details Windows 1 Runtheinstaller named ChenomxNmrSuite Edition 5 0 windows setup exe 2 Followthe instructions displayed on screen 3 You have now installed Chenomx NMR Suite Linux 32 bit 1 Copy
207. s to fit the selected region If the region you are trying to fit cannot be accurately modeled using 100 peaks you can try selecting 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 Add Peak on page 76 9 3 Fitting Tools 80 CHENOMX NMR SUITE USER MANUAL e Selecting Peaks and Clusters on page 77 e Adjusting Peaks on page 78 e Optimize Selected Peak Shapes on page 79 Transform Windows You can set limits on the amounts that you can transform or move individual clusters in a compound signature in Profiler These limits are called transform windows Establishing transform windows for your own compounds improves the quality of fits that you perform with your custom compound signatures When you set transform windows you should 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 ifyou routinely analyze spectra with widely varying pH you generally need larger transform windows than if your sample spectra are always close to neutral The most common influences on the position of a cluster in a compound are pH and ion concentrations In order to set accurate transform windows for a compound you should consider acquiring spectra of the pure compound at the outer limits of the conditions you expect to encoun
208. same collection of compound signatures How do export a compound pack from the current spectrum 1 Openthe Export Profiled Compounds dialog 2 Enteranameforthe 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 3 ClickOK 4 Intheresulting file chooser locate the folder in which you would like to save the compound pack 5 Inthe File Name field type the new name for the compound pack file This can be different from the name of the compound pack itself but you may prefer to keep them the same 6 ClickSave Tips and Tricks e You and your collaborator each need a valid licensed copy of Chenomx NMR Suite installed in order to make use of compound packs 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 44 e Import Compounds on page 89 e Export as Compound Pack on page 90 e Compound Sets on page 94 Import Profile When you are fitting a series of spectra from the same study the spectra are often quite similar to one another While itis possible to fit each spectrum from scratch it can be much more efficient to copy a fit from an earlier spectrum in the series and then adjust it to match the current spectrum Importing profil
209. se partially exposed peaks to establish positions for each of the overlapped clusters Starting with the approximate fit thus obtained fine tune the position and height of each of the overlapped clusters to optimize the overall fit in the region Generally fit 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 fit may be unreliable especially if most or all of the clusters are low intensity singlets 11 4 Tutorial Targeted Profiling 111 CHENOMX NMR SUITE USER MANUAL Overlap Region Contributing Compounds 1 Serine 2 Glycolate 3 Pantothenate nf li Fo t hh ig l Ni NM BENI l VU A NWN NN T T T 4 00 3 95 3 90 Figure 11 4 Using frequency filters and sorting by potential concentration allow identifying serine glycolate and pantothenate as candidate compounds Visual comparison of the signatures to the spectrum line confirms the identifications Compound Lines Sum Line Blue Serine Serine 968 uM Green Glycolate Glycolate 704 uM Purple Pantothenate Pantothenate 104 uM KAA A T T T T T T 4 00 3 95 3 90 4 00 3 95 3 90 Figure 11 5 Fitting 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
210. sing 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 remaining two serine clusters using the frequency controls 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 so that the sum line fits the spectrum Since the multi peak compounds in the region are already well fit setting an appropriate height for glycolate should now be quite simple Select fucose display the cluster near 3 7 ppm and adjust it using the frequency control In the Compound Table select alanine and set it to its potential concentration Display the alanine cluster near 1 5 ppm and adjust it to fit 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 use the frequency control to match it to the spectrum using the sum line to evaluate your progress Adjust each of the fucose clusters near 3 8 ppm using the frequency controls Try finding individual peaks in each cluster that match peaks in the spectrum and lining them up Adjust each of the remaining fucose clusters using the frequency controls If there is not enough of a pattern visible in the spectrum to match a clu
211. sitions TSP spectrum indicating 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 ofthe compound lines in the profile of the currently open spectrum colored red by default Profiling technique needed for fitting overlapped regions Clusters overlapping in a particular region are manipulated 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 Macro available for VNMR and VNMRj that saves the phasefile for a spectrum alongside its raw data fid in a subfolder called datdir See scalable vector graphics See compressed scalable vector graphics See standardized width Variation of spectral binning in which the bins are defined as the transform windows of each cluster of each compound in a compound set Data reduction method embodied in the Profiler module involving comparison ofa spectrum to compound signatures in your Library reducing spectral data to a list of quantified compounds Aquick 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
212. ster by 5096 Profiler reduces the heights of all of the other clusters for the compound by 50 5 fany of the clusters for the current compound overlap with compounds that you have already fit you may need to readjust those compounds 4 5 Determining Compound Concentrations 15 Chapter 5 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 These include basic file operations navigation display options and preferences that directly affect your day to day use of Chenomx NMR Suite 5 1 Opening a File You can open 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 Open the file selection dialog Locate the folder containing the spectrum Select the file and click Open u e w N If the file you are opening requires importing select import options as necessary Tips and Tricks e If
213. ster to leave the cluster in its original position In the Compound Table select urea and set it to its potential concentration Adjust the urea cluster near 5 8 ppm to match it to the spectrum Check the overall fit 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 11 2 Expected Concentrations for Advanced Start cnx Compound Conc mM Compound Conc mM 2 Oxoglutarate 0 5047 Fumarate 0 1242 3 Indoxylsulfate 0 3683 Glycolate 0 6904 4 Hydroxy 3 methoxymandelate 0 0429 Niacinamide 0 4704 11 3 Tutorial Profiler 107 CHE OMX NMR SUITE USER MANUAL Compound Conc mM Compound Conc mM Acetate 0 4928 Pantothenate 0 0824 Alanine 0 5314 Pyruvate 0 4730 Citrate 0 4370 Serine 0 9652 DSS Chemical Shape Indicator 0 4853 Taurine 0 9906 Dimethylamine 0 5299 Threonine 0 3484 Formate 0 2529 Trimethylamine 0 4976 Fucose 0 5009 Urea 332 2911 Bonus fit There are at least two additional compounds present in trace quantities in this spectrum Identify and fit these compounds and check their concentrations here Compound 1 0 0498 mM Compound 2 0 0109 mM 11 4 Tutorial Targeted Profiling Targeted profiling involves fitti
214. t to minimize its interference with other fits in the spectrum 4 5 Determining Compound Concentrations Once you have identified compounds present in a sample you need to determine their concentrations based on the data in the spectrum For more details on techniques for determining optimal fits of compounds in experimental spectra see Tutorial Targeted Profiling on page 108 To determine the concentration of a compound 1 Ifthe subtraction line green is not currently visible turn it on via the View menu 2 Seta concentration for the compound so that you can see the clusters clearly see Concentrations on page 49 3 Use the Cluster Navigator to locate a cluster that you can use to approximate the compound concentration see Cluster Navigator on page 53 When choosing a cluster with which to establish a compound s concentration you should use a cluster that overlaps others clusters as little as possible 4 Clickand 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 110 Profiler applies any adjustments that you make to the height of one cluster proportionately to all of the clusters for the compound For example if you reduce the height of one clu
215. te 12 13 14 15 16 17 18 19 Zoom in on the single peak near 2 40 ppm Right click on the peak and click Filter for Compounds Near 2 36 ppm In the Compound Table select pyruvate Click the location of the peak 2 4 ppm in the Cluster Navigator to include the peak s full range of motion in the Spectrum View Set pyruvate to its potential concentration Click and drag the pyruvate signature blue to match it as closely as possible to the corresponding peak in the spectrum black Clear the quick search box above the Compound Table by clicking the red X Click Show Entire Spectrum Compensating for Water Suppression Effects Alanine 20 21 22 23 24 25 26 27 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 Click the location of the doublet 1 5 ppm in the Cluster Navigator to include the doublet s full range of motion in the Spectrum View Set alanine to its potential concentration Click and drag the alanine doublet blue to match it as closely as possible to 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 Click the location ofthe second cluster of alanine 3 8 ppm in the Cluster Navigator to zoom to it in the Spectrum View Use
216. tely 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 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 a fit 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 allowing binning results to be compared across multiple spectra Bins can be normalized 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 creatinine signal then the intensity of the urea signalis 0 5 ni 133 CHENOMX NMR SUITE USER MANUAL evomx O optimize selected peak shapes pack pdf peak pH editor pH indicator phase correction phasefile phasing png portable document format po
217. ter that describes the pH over which a compound signature is expected to accurately reflect an experimental spectrum Often correlated 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 spectrometers 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 This should not be confused with water subtraction methods operating in the time domain to remove the water signal itself water suppression Technique used to reduce the contribution of the water signal to 1H NMR spectra of aqueous solutions via a special pulse sequences X 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 140 CHENOMX NMR SUITE USER MANUAL number of points that is a power of 2 enabling the use of fast Fourier transform algorithms Can also be used to increase the digital resolution of a sp
218. ter when fitting the compounds in experimental mixtures This allows you to map the maximum extent of these effects on the cluster positions in your compounds In the absence of specific information about the behaviour of a cluster you can set a default transform window for the cluster This sets a transform window 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 I set the transform window for a cluster Compound gt Transform Window 1 Menu Location gt Edit for Selected Cluster Select the cluster for which you would like to set a transform window Eae 2 Openthe Edit Transform Window dialog 3 Select Limit transforms to and enter the new lower and upper limits for the selected cluster 4 ClickOK How do I change the transform window for a cluster 1 Selectthe cluster whose transform window you would like to change 2 Openthe Edit Transform Window dialog 3 Enterthe new lower and upper limits for the selected cluster 4 Click OK How do I set the default transform window for a cluster 7 EM C ooo 1 Selectthe cluster for which you would like to set the transform window enu Location Set Default on Selected d RS 2 Onthe Compound menu select Transform Window Set Default on Selected Icon s Cluster Compound gt Transform Window How do
219. ters on page 77 Adjusting Peaks In most cases your initial placement of a peak does not allow a sufficiently accurate fit of the overlaid spectrum You need to modify the height or frequency of one or more peaks to arrive at a fit that satisfies your requirements How do I set peak properties to specific values Menu Location Compound gt Edit Selected 1 Select the peaks or clusters that you would like to adjust VOIE 2d 2 Openthe Edit Selected Peaks dialog Ctrl E 3 Enterthe desired center position in ppm amplitude height in si and width in Fonero Cmd E sw to apply to all selected peaks or clusters 4 ClickOK How do adjust peak properties with the mouse 1 Selectthe peaks or clusters that you would like to adjust 2 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 3 Click and drag the blue triangles on either side of the selected peaks and clusters at approximately half height to adjust their widths Tips and Tricks e When you enter specific values in the Edit Selected Peaks dialog the values that you enter are applied to all of the selected peaks regardless of which clusters they are associated with 9 3 Fitting Tools 78 CHENOMX NMR SUITE USER MANUAL e Double click on a peak or cluster in the Information Panel
220. th Compound Sets and Smart Compound Sets when you no longer have need for them 10 4 Compound Set Tools 97 CHENOMX NMR SUITE USER MANUAL How do I delete a Compound Set or Smart Compound Set EL lle Delete Compound Set 1 Selecta Compound Set or Smart Compound Set in the Compound Set Panel oni n 2 ClickDelete Compound Set Tips and Tricks e Right click on the name ofa Compound Set or Smart Compound Set and select Delete to delete the set Related Topics e Compound Set Panel on page 93 e Compound Sets on page 94 e Smart Compound Sets on page 95 10 4 Compound Set Tools 98 Chapter 11 Tutorials Whether you are a brand new user of Chenomx NMR Suite or you have just upgraded from an earlier version the tutorials in this chapter can help you use any ofthe available modules more effectively 11 1 File Location Note Linux Windows You can find all files mentioned in these tutorials in the Samplesw folder in your Chenomx NMR Suite install folder Mac You can find all files mentioned in these tutorials in the Samples folder in your Chenomx NMR Suite DMG image 11 2 Tutorial 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 you should add spectrum metadata The most important metadata you should add is a CSI definition Processor adds some spect
221. the Export Profiled Concentrations 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 Choose the compounds for which you would like to export concentration 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 of the 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 a file called concentrations txt is created in the folder containing your source spectra 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 values open the spectrum in Processor and use the pH editor The value that you set in the pH editor appears in the exp
222. the number of points originally saved in a spectrum if it was pre 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 Limit placed on the extent of transforms possible on a particular cluster Lorentzian 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 139 CHENOMX NMR SUITE USER MANUAL ENOMX U uncoupled split 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 universally unique Standard identifier commonly used in software to ensure that a identifier piece of information like a compound signature can be identified in such a way that the same identifier will never be used for another piece of information unprocessed spectrum Raw data from spectra acquired using Bruker or Varian data spectrometers that UUID See universally unique identifier valid pH range Optional parame
223. theinstallerscript named ChenomxNmrSuite Edition 5 0 linux x86 sh to your desired installation folder 2 RunChenomxNmrSuite Edition 5 0 linux x86 sh 3 The install script creates a new folder named ChenomxNmrSuite Edition you can run Chenomx NMR Suite by running the ChenomxNmrSuite sh script located in this folder 4 You have now installed Chenomx NMR Suite Linux 64 bit 1 Copythe installer script named ChenomxNmrSuite Edition 5 0 linux x86 64 sh to your desired installation folder 2 RunChenomxNmrSuite Edition 5 0 linux x86 64 sh 3 Anew folder named ChenomxNmrSuite Edition is created 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 2 Activation and Licensing Chenomx NMR Suite uses an activation system Activation is an anti piracy technology designed to verify that Chenomx software products are legitimately licensed After you 1 1 Installation 1 evomx CHENOMX NMR SUITE USER MANUAL install the Chenomx NMR Suite software you need to activate it to ensure that you can use all of the modules and libraries that you purchased and that you can open edit and save changes to files other than Chenomx demo files To activate Chenomx NMR Suite Menu Location Icon s Help gt Activation Details D Li 1 Open any module of Chenomx NMR Suite If you have not previously activated or
224. to Zoom Menu Location View Zoom Auto Zoom Auto Zoom allows you to quickly adjust the vertical scale of the current view so that the Icon s y VEN s tallest peak in the currently displayed frequency range fits in the viewing pane without Ctrl F changing the displayed frequency range Hotkey s ETT 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 View Zoom Increase Decrease Vertical2Zoom ncrease Decrease Vertical Zoom allows you to incrementally adjust the vertical scale of Lon Te the current view without changing the displayed frequency range Menu Location Tips and Tricks Hotkey s plus or minus e Decrease Vertical Zoom is not available when the full spectrum is displayed 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 o
225. to open the Edit Selected Peaks dialog for the double clicked item e Right click on a selection in the Spectrum View or Information Pane and select Edit Selected Peaks to edit properties for the selection Related Topics e Add Peak on page 76 e Selecting Peaks and Clusters on page 77 e Grouping Peaks as a Cluster on page 79 e Optimize Selected Peak Shapes on page 79 e Generate Cluster for Region on page 80 e Transform Windows on page 81 e Cluster Navigator on page 82 Grouping Peaks as a Cluster During the fitting process and especially when you are fitting more complex compounds you may need to group peaks from one or more clusters into a cluster of their own This ensures that all of the 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 Menu Location dc ned 1 Selectthe peaks and clusters that you would like to group as a new cluster eaks as Cluster Icon s a 2 Click Group Selected Peaks as Cluster Ctri G Hotkey s s Tips and Tricks e Right click on a selection in the Spectrum View or Information Pane 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
226. tra 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 16 Processing History on page 32 e Processing Tools on page 34 Send to Profiler When you finish processing a spectrum in Processor your nexttask is often to start profiling er OOGA File gt 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 7 Profiler on page 41
227. tration accurately 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 Spectra that are poorly collected or collected from samples that are poorly prepared may be difficult or even impossible to convert and analyze accurately Accurate analysis of your NMR spectra with Chenomx NMR Suite requires good sample preparation and the acquisition of high quality spectra 3 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 to allow accurate quantification using Chenomx NMR Suite The internal standard solution recommended for use with Chenomx NMR Suite contains the following components e 99 9 D5O as a solvent to allow locking during spectral acquisition e 5 mM 22 Dimethyl 2 silapentane 5 sulfonate DSS as a chemical shape indicator CSI e 0 2 w v sodium azide NaN3 to inhibit bacterial growth e Optional 100 mM imidazole as a pH indicator e Optional 100 mM creatinine as a pH indicator e Optional 100 mM DFTMP as a pH indicator You should adjust the pH of the above mixture to about 6 5 and add itas a 1 in 10 1096 v v spike to each of your samples to yield 1096 D 0 0 5 mM DSS 0 02 w v NaN and 10 mM imidazole creatinine or DFTMP if present Instead of DSS
228. trum Thumbnail outside the zoom box to show the entire spectrum in the Spectrum View This is the same as using the Show Entire Spectrum zoom tool e Double click anywhere in the Spectrum Thumbnail to show the entire spectrum in the Spectrum View This is the same as using the Show Entire Spectrum tool Select Region You can use the Select Region tool as an alternate zoom function as well as to specify areas with which to filter the Compound Table How do I select a region Menu Location Icon s Hotkey s VIEW gt SelectRggigN 1 Activate Select Region iii I 2 Click and drag across a region of the Spectrum View to define a selected region p 3 Double click in the selected region to expand the region horizontally to fill the md Spectrum View Or Middle click in the selected region to expand the region horizontally to fill the Spectrum View and apply an Auto Zoom Tips and Tricks e You can also activate Select Region by double clicking anywhere in the Spectrum View Tape Measure All modules include a simple tape measure that you can use to measure differences between two points in the Spectrum View displayed in both Hz and ppm How do measure frequency differences in the Spectrum View 1 Pressand hold down the Shift key 2 Clickin the Spectrum View where you would like to start a measurement then drag to the end point 5 9 Spectrum View Tools 22 CHENOMX NMR SUITE USER MANUAL Tip
229. u Location File Import 1 Icon s 2 3 4 5 Open the Import Compound dialog Locate the folder containing the simulation or album file that you would like to import 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 9 3 Fitting Tools 75 exomx CHENOMX NMR SUITE USER MANUAL Tips and Tricks e 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 e You should calibrate a signature to a real spectrum for more accurate results when using the signature in an analysis Related Topics e Overlaying a Spectrum on page 19 e Chapter 8 Spin Simulator on page 63 e Compound Details on page 84 Add Peak Add Peak allows you to add a new peak to the current compound signature The mouse cursor changes to a large crosshair and the next point that you click in the Spectrum View defines the position and height for the new peak The new peak appears in the peaks list is 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 C
230. umber of data points in a Chenomx spectrum after data has been imported and zero filling applied In Profiler a quick search based on the position of peaks in the spectrum in ppm Can be used to specify a single frequency ora range of frequencies resulting in a list of all compounds having at least 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 fit the selected region based on minimizing the average intensity of the subtraction line 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 2 3 and a J value of 5 67 Hz average of 4 6 and 7 Hz In Compound Builder defines 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 131 CHENOMX NMR SUITE USER MANUAL evomx H highlight lines highlighted compound imidazole importing compounds InChl IUPAC international chemical identifier Java runtime environment JCAMP DX spectrum data jdf
231. und Set Panel If you set a profiled compound s concentration to unknown Profiler removes the compound from the Profiled Compounds set How do set compound concentrations 1 Selecta 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 2 Click and drag the blue triangle at the far right of the Spectrum View upward until the compound signature reaches the desired height If the compound already has a concentration 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 the Profiled Compounds setis selected If you still do not see any compounds with concentrations then the current file has no concentrations set 2 Inthe Compounds 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 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 or type to set the concentration to unknown e Once you have set
232. uple SD3 to SD2 18 Add a jJ 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 11 5 Tutorial Spin Simulator 119 evomx CHENOMX NMR SUITE USER MANUAL 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 here 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 of the 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 fo
233. ur library These 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 6 to 8 added to the library after January 1 2008 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 10 4 Compound Set Tools 95 evomx CHENOMX NMR SUITE USER MANUAL H
234. use Chenomx NMR Suite the most 2 1 Signature Builder The capabilities formerly found in Signature Builder have been divided into two modules Spin Simulator and Compound Builder Spin Simulator allows you to build theoretical models of compounds using coupling relationships while Compound Builder includes free form fitting tools and automation algorithms to fit overall cluster shapes without direct reference to the theoretical underpinnings of a compound s spectrum 2 2 Spin Simulator Spin Simulator is a new module that inherited the theoretical basis of creating compound signatures from Signature Builder The simple first order simulation performed by Signature Builder has been replaced with full quantum mechanical spin simulation which models higher order effects using spin definitions and spin spin coupling allowing more accurate simulations To create compound signatures that are applicable outside a very narrow range of spectrum conditions you will need to simulate the compound in Spin Simulator then open the simulation in Compound Builder for refinement You can then save the refined fit as a compound file xcpd and add itto your library 2 3 Compound Builder Compound Builder is a new module that inherited the free form and automated Lorentzian fitting tools from Signature Builder Compound Builder focuses on making it easy to add new compounds to your compound library Modeling a compound is a simple fast process that no lo
235. 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 OpenLibrary Manager 2 Click Compounds Import 11 7 Tutorial Library Manager 126 evomx CHENOMX NMR SUITE USER MANUAL 3 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 4 Select your compound files and click Choose Files If you are using the sample files select Valine xcpd and Proline xcpd and click Choose Files 5 Click Next 6 Click the Create associated compound set check box and enter a name for the new 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 entered a compound set it appears in the Compound Set Table Otherwise you can find your newly add compounds in the Compounds set at the top of the Compound Set Table You can use the same technique 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 comp
236. 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 Page description language introduced by Adobe Systems Incorporated for describing images in a device independent way Used primarily for electronic and professional desktop publishing Estimated upper limit of a compound s concentration calculated automatically by Profiler Potential concentrations can be used to guide profiling of a spectrum In Processor an entry that appears in the Processing History to indicate prior processing in third party software packages 134 CHENOMX NMR SUITE USER MANUAL Processing History processing layer Processor profile profiled compounds Profiler proxy server ps pulse sequence Q quick search Appears when processed data is imported 1r phasefile ft2 jdf jdx In Processor a panel showing the processing layers that have been applied to the currently open spectrum Also allows reviewing the details of each layer and removing layers as needed In Processor one of several modifications that can be made 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 Module in Chenom
237. x NMR Suite used to 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 including concentrations transforms custom colors highlights and stars Also compounds that appear in the Profiled Compounds set in the Compound Set Panel Module in Chenomx NMR Suite used to analyze spectra by comparison with compound signatures from your Library creating a profile of the spectrum in a process called targeted profiling 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 vi
238. y flexible task You can vary the number of compounds fit to a particular spectrum to suit a variety of timeframes research goals or other requirements One ofthe most important aspects of your approach to fitting a spectrum should be maintaining a consistent fitting strategy as this gives you more consistent and more easily interpreted results For more details on specific fitting techniques and how to apply them to your spectra please see Tutorial Targeted Profiling on page 108 To fit a spectrum using targeted profiling 1 Processthe spectrum see Processing a Spectrum on page 11 2 Optional Create a Smart Compound Set or Compound Set containing the compounds that you would like to analyze see Chapter 10 Library Manager on page 86 3 Open the spectrum in Profiler see Opening a File on page 16 4 Selecta Compound Set containing compounds appropriate for the sample If you created a Compound Set or Smart Compound Set above select the Compound Set that you created 5 Identify and fit prominent signals in the spectrum see Identifying Compounds on page 12 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 fit as needed You can
239. y spectrum If you choose to use line broadening you should do so after phasing and baseline correction While importing a spectrum you may choose to have Processor automatically apply line broadening of 0 to 1000 Hz Otherwise you can apply line broadening manually after you have imported the spectrum In either case a Line Broadening layer appears in the Processing History you can remove the layer if necessary How do apply line broadening to my spectrum Menu Location Icon s Hotkey s Processing Line Broadening 1 T 2 Ctrl Alt 3 3 Cmd Alt 3 Switch to Line Broadening mode Enter a value between 0 and 1000 Hz Click the Accept button Tips and Tricks If you intend to apply reference deconvolution to your spectrum you can add line broadening at the same time See Reference Deconvolution on page 37 for details 6 4 Processing Tools 36 CHENOMX NMR SUITE USER MANUAL Related Topics Importing Spectra on page 16 e Processing History on page 32 e Phasing on page 34 e Baseline Correction on page 35 Reference Deconvolution on page 37 e Convert Spectra on page 39 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 i
240. you are opening a Varian spectrum named Example fid the raw data is stored in the file named Example fid fid while the processed data is stored in the file named Example fid datdir phasefile e Ifyou are opening a Bruker spectrum named Example 1 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 5 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 t2 or JCAMP DX jdx file formats When you import processed spectra your import options are somewhat limited since most of the processing that you may want to apply is assumed to have already taken place 5 1 Opening a File 16 Qe ow CHENOMX NMR SUITE USER MANUAL Table 5 1 Import NMR Data Options CSI Concentration mM pH Auto pH Advanced Details Defaults Specify the Chemical Shape Indicator CSI used in the sample You can choose DSS TSP or formate Enter the concentration ofthe specified CSI in millimoles per litre Attempt to automatically detect the pH of the sample using signals from imidazole creatinine and DFTMP You must have at

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