Thank you for purchasing Chenomx NMR Suite, an integrated set of tools that allows you to easily identify and quantify compounds in NMR spectra. By combining sophisticated chemistry with advanced algorithms, Chenomx NMR Suite offers you a metabolic profiling platform with unparalleled power and ease of use.

This guide is divided into the following sections:

Chenomx NMR Suite icon

Chenomx NMR Suite is an integrated suite of tools that allows you to easily identify and quantify compounds in NMR spectra. The following products make up Chenomx NMR Suite:

Chenomx Profiler icon

Chenomx Profiler offers you a broad range of tools to assist in identifying and quantifying compound concentrations based on data in an NMR spectrum.

Using a compound library of over 260 unique spectral signatures together with sophisticated computer-assisted fitting routines, you can accomplish in minutes what would have taken hours or days using manual analysis methods.

Chenomx Spin Simulator icon

Chenomx Spin Simulator is a simple yet powerful tool for creating simulations of NMR spectra, based on user-defined spin systems, coupling relationships and reference spectra. You can use these simulations as starting points for creating your own compound signatures based on fundamentals of NMR theory.

Chenomx Compound Builder icon

Chenomx Compound Builder is a tool for creating custom compound signatures. You can use Compound Builder to model compounds of interest that are not present in the standard Chenomx compound library, and use these signatures in later analyses in Profiler. Free-form editing tools and automated algorithms help you to quickly create rough models from scratch, or refine theoretical models from Spin Simulator to match your particular sample type or acquisition conditions.

Chenomx Library Manager icon

Chenomx Library Manager allows you to create and manage Compound Sets for use in Profiler. Compound Sets can contain any compound signatures in your library, including those from the Chenomx library as well as those that you create with Compound Builder.

You can tailor a Compound Set to a specific project. For example, in a research project, you may only be interested in examining the concentrations of five particular compounds for a drug study; you can use Library Manager to create a Compound Set including only those compounds.

Chenomx Processor icon

Chenomx Processor allows you to convert a variety of native spectrum formats into the Chenomx file format. Supported formats include:

  • Varian VNMR (fid and phasefile)

  • Bruker XWIN-NMR (fid and 1r)

  • JEOL Delta (.jdf)

  • NMRPipe (.fid and .ft2)

  • JCAMP-DX (.jdf, version 5.0 and above)

In addition, Processor allows you to identify or manually override the automatically determined parameters for the chemical shape indicator (CSI) and sample pH. You can also apply a variety of processing layers, including phasing, linear or cubic spline baseline correction, reference deconvolution and exponential fid weighting (line broadening).

Compound Builder icon
  • 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.
Spin Simulator icon
  • 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. Spin Simulator can export simulations to Compound Builder for "fine-tuning" before they are used in Profiler.
Compound Builder icon
  • 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 longer requires fully assigning a compound and deciphering all of its coupling relationships before you start creating a new compound.
Library Manager icon
  • Library Manager » Library Manager has been redesigned from the ground up to make compound and compound list management as intuitive and as powerful as possible. Creating "Compound Sets" that contain a set of compounds specific to a sample type or study is a simple drag-and-drop. "Smart Compound Sets" can be created to automatically filter the compound library to a set of compounds that match specified criteria.
  • New Compound Library Format » The compound library format used by Chenomx NMR Suite has been completely redesigned. The compound library is now simply a folder made up of one or more Chenomx Compound files (.xcpd). Adding or removing compounds from your compound library is as simple as adding or removing compounds from the library folder.
Profiler icon
  • Smaller and Faster Spectrum Files » Previous versions of Chenomx NMR Suite "embedded" a copy of the compound library in each spectrum file (.cnx). Chenomx NMR Suite 5.0 makes spectrum files smaller and faster to load by only storing references to a compound in the spectrum file itself; the compound is then loaded on demand when the file is opened in Profiler.
Chenomx NMR Suite icon
  • Set Zoom Region » It is now possible to set the zoom region based on user-specified ranges (horizontal and vertical).
  • Selected Region » The selected region can now be resized by grabbing and moving its edges.
  • Internet-Enabled Reference Panel » The Reference Panel now automatically retrieves compound-specific information from the Internet, meaning the Reference Panel is always expanding and improving as we retrieve new information for individual compounds.
  • Enhanced Cluster Navigator » You can set the view to encompass multiple clusters by clicking and dragging them in the Cluster Navigator.
Chenomx Profiler icon
  • Improved Compound Interface » Compounds are now displayed as filled-in shapes that can be easily manipulated.
  • Improved Compound Selection » Selecting a compound of interest in a heavily-overlapped region has been improved. Clicking the area under the sum line automatically cycles through the compounds that contribute to the sum area. Right-clicking the sum area will provide a context-sensitive menu that provides information on all compounds contributing to the signal in that region.
  • Improved Export Spectrum Graphic » Exporting spectrum graphics is now an easy-to-use wizard.
  • Improved Spectral Binning » Spectral binning is now easier than ever with the new spectral binning wizard.
  • Compound Versioning » Identifying and reconciling out-of-date compounds is now possible with Profiler's new compound versioning support.
  • Compound Coloring » Assign custom colors to compounds, and pin them to the Spectrum View with Profiler's Custom Color and Highlight annotations.
  • Compound "Starring" » Note important compounds using Profiler's "starring" tool.
Chenomx Processor icon
  • DFTMP » DFTMP has been added to Processor's list of supported pH indicators.
Chenomx Library Manager icon

Chenomx NMR Suite requires a Java Runtime Environment. Please download and install the latest version of Java from Sun Microsystems. For Mac OS X, please use the latest version of Java supplied by Apple.

After installing the software, you need to activate it, and install the compound libraries that you have licensed. Please see Activating Chenomx NMR Suite and Installing the Chenomx Compound Library for more details.

Windows XP product icon

  1. From the install CD, run \windows\ChenomxNmrSuite[Edition]-5.0-windows-setup.exe.

  2. Follow the instructions displayed on screen.

  3. You have now installed Chenomx NMR Suite!

Mac OS X product icon

  1. From the install CD, open the DMG file /osx/ChenomxNmrSuite[Edition]-5.0-osx.dmg.

  2. Drag and drop the "Chenomx NMR Suite" application bundle to your desired installation location.

  3. You have now installed Chenomx NMR Suite!

Linux penguin icon

  1. From the install CD, copy /linux-x86/ChenomxNmrSuite[Edition]-5.0-linux-x86.sh to your desired installation folder.

  2. Run ChenomxNmrSuite[Edition]-5.0-linux-x86.sh.

  3. A new 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!

Solaris 10 product icon

  1. From the install CD, copy /solaris-sparc/ChenomxNmrSuite[Edition]-5.0-solaris-sparc.sh to your desired installation folder.

  2. Run ChenomxNmrSuite[Edition]-5.0-solaris-sparc.sh.

  3. A new 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!

After you install the Chenomx NMR Suite software, you need to activate it. Activation ensures 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

  1. Open any module of Chenomx NMR Suite. The Chenomx License Activation dialog appears.

  2. Send the activation key listed in the dialog to Chenomx Technical Support at +1 780 432 0033 or .

    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.

  3. You will receive a license file (.cnxlic) from a support staff member. Save the license file to a folder on your computer.
  4. Open any module of Chenomx NMR Suite. The Chenomx License Activation dialog appears again.
  5. Click the Select License File button.
  6. Browse to the folder in which you saved the license file, select the file, and click the Open button.
  7. 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 Activation Details on the Help menu in any module.

Due to the variety of compound libraries available, Chenomx does not distribute compound libraries as part of the Chenomx NMR Suite installer. Your compound libraries should be included on your installation CD in the Libraries folder; if not, you will receive the compound libraries that you have licensed separately (either on CD, via e-mail, or via a web download).

If you have not received the compound libraries that you have licensed, please contact Chenomx Technical Support at +1 780 432 0033 or .

To install the Chenomx Compound Library

  1. Save your Chenomx compound packs (.pack) to a folder accessible to the computer on which you have installed Chenomx NMR Suite.

  2. Open the Library Manager module of Chenomx NMR Suite.

  3. On the Compounds menu, click Import...

  4. Click the Browse button (...), and navigate to the folder in which you saved your Chenomx compound packs (.pack).

  5. Select the compound packs that you would like to install, and click Choose Files.

  6. Click Next.

  7. 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.

  8. Click Finish.

One of the best ways to get familiar with the Chenomx NMR Suite platform is to try the tutorials.

To access the tutorials, please see the "Tutorials" section of the Chenomx NMR Suite User Guide (Note: these tutorials are also available in the Chenomx NMR Suite online help).

The standalone Chenomx NMR Suite documentation (.pdf) is stored in the Documentation subfolder of the folder you specified during installation of Chenomx NMR Suite.

Please note that the standalone Chenomx NMR Suite documentation requires the free Adobe Acrobat Reader or equivalent.