Compound Discoverer 3.2 Installation Instructions

Thermo Compound Discoverer™ is a licensed application that can be used for up to 60 days without activating the software license after installation.

Upon ordering, you will receive a software media kit with a key-shaped USB flash drive containing the installation executable. An email from Thermo MS Licensing will provide the necessary information to activate your software license.

If you are upgrading from a previous version, the software installer and license can be found on the LSMS Software Download and Licensing Portal.

Important Information

• The installation requires Windows 7 SP1 64-bit or Windows 10 64-bit operating system.
• The Compound Discoverer 3.2 licensing process requires an Internet connection for validation. Installation can be done on a computer without internet access, with activation completed on a computer that has internet access.
• The Compound Discoverer application supports US-English Only locale.

Note: Versions 1.0, 2.0, 2.1, 3.0, 3.1, and 3.2 of the Compound Discoverer application can coexist on the same computer.

The installation executable includes three installers: the Thermo Compound Discoverer 3.2 installer, the Thermo mzCloud™ Offline Library installer (which installs four mzVault libraries that are July 2020 snapshots of the online mzCloud mass spectral database), and the Thermo mzVault installer (which installs the mzVault application).

Contents

• Installing the Compound Discoverer application
• Installing the mzCloud Offline libraries
• Installing the mzVault 2.3 application
• NIST libraries for GC EI Orbitrap data
• Activating the software license

To install the Compound Discoverer application

Option 1: Using USB Flash Drive

1. Insert the Compound Discoverer USB flash drive into a USB port on your computer.
2. Open Windows Explorer and select the USB drive to view its contents.
3. Locate the executable: XStart_Compound Discoverer.exe.
4. Double-click XStart_Compound Discoverer.exe to start the installation wizard.

Option 2: Downloading from the Web Portal

1. Go to the website: https://thermo.flexnetoperations.com.
2. Log in to your account. If you do not have an account, click Register.
3. On the left side of the Life Sciences Mass Spectrometry Software Download and Licensing Portal, click Product List under Software and Services.
4. On the Product List page, click the Demo hyperlink.
5. On the Product Information page, click the Compound Discoverer 3.2 hyperlink.
6. On the Product Download page, in the File Name column, click the down arrow to the left of Compound Discoverer 3.2.zip, click Save As, and save the compressed folder to your computer.
7. Extract the contents of the zipped folder and locate the executable: XStart_Compound Discoverer.exe.
8. Double-click XStart_Compound Discoverer.exe to start the installation wizard.

The installation wizard will begin. The installer also provides access to other documents as PDF files: Release Notes, Installation Instructions, user guides, tutorials, and licensing information. A PDF document viewer is required.

Figure 1: Compound Discoverer installation wizard shows the main installation window with options to install Compound Discoverer 3.2, mzVault 2.3, and the mzCloud Offline Library, along with other related software like Microsoft .NET Framework.

Follow the on-screen instructions in the installer. The Minimum Product Requirements screen will appear, summarizing the system's compatibility. If all requirements are met, a confirmation message will be displayed.

At the Installation Qualification prompt, click Yes to view the report or No to skip it.

Upon completion, select whether to restart your computer and then click Finish.

Installing the mzCloud Offline libraries

1. If the installer restarted your computer, double-click XStart_Compound Discoverer.exe to restart the installer.
2. Click mzCloud Offline Library Installer to install the mzCloud Offline libraries.
3. Restart your computer if you did not restart it after installing the Compound Discoverer application.

Installing the mzVault 2.3 application

To create mass spectral libraries from your own data acquired with a high-resolution accurate-mass (HRAM) Thermo Scientific mass spectrometer, install the mzVault 2.3 application. The Compound Discoverer installer includes an installer for the mzVault application.

To install the mzVault application:

1. If the Compound Discoverer installer is not open, open it by locating and double-clicking the XStart_Compound Discoverer.exe executable (found on the USB drive or in the downloaded zip folder).
2. Click mzVault 2.3. The Thermo mzVault Installshield Wizard will open.

Note: If you have an earlier version of mzVault, follow the instructions to remove it before installing mzVault 2.3.

If your computer meets the minimum requirements, the Next button will become available. Click Next to continue.

When the installation is complete, click Finish.

NIST libraries for GC EI Orbitrap data

To process GC EI Orbitrap data with Compound Discoverer, Thermo Fisher Scientific recommends installing at least one NIST MS Search formatted EI MS library. These libraries are not included with Compound Discoverer and must be purchased separately from third-party vendors and installed within the NIST MS Search folder.

Activating the software license

To activate your Compound Discoverer 3.2 software license, you need the product ID (e.g., XCALI-XXXXX) and the activation code. You should receive an email from Thermo MS Licensing with the subject line “Your Order Is Ready” within one week of ordering the software. This email contains the product ID and activation code.

Entering the product ID and the activation Code

Follow one of these topics:

• Activating the license on an online computer
• Activating the license on an offline computer

To enter the licensing information:

1. From the application menu bar, choose Help > License Manager. The License Manager opens as a tabbed document.
2. On the License Manager page, click Activate. The License Activation dialog box opens to the Activation Code view.

Figure 2: License Manager page shows the License Manager interface with listed licenses and their status. Figure 3: License Activation dialog box opened to the Activation Code view displays the fields for entering activation details.

In the Activation Code view:

• Locate the email from Thermo MS Licensing with “Your Order is Ready” in the subject line for your product ID and activation code.
• Enter the company name, your full name, and email address.
• Enter the product ID and activation code.
• If the computer connects to the Internet, click Online Activation.
• If the computer does not connect to the Internet, click Offline Activation and follow the instructions to process a response file (activation.xml).

If you have not received your activation code:

• Check your Junk Email folder.
• If the email is not in your Junk Email folder, log in to your account at https://thermo.flexnetoperations.com. Under Software & Services, click Order History, then click the order number for the ordered products.
• If you cannot find your account, send an email to ThermoMSLicensing@thermofisher.com with the following details: Software application (Compound Discoverer), sales order number or purchase order number, end user name, and end user email.

In the License Activation dialog box, enter your company name, full name, contact email address, the product ID for Compound Discoverer 3.2, and the activation code. There are several product IDs available, including those for software upgrades. Refer to Table 1 for Product IDs.

Table 1: Product IDs for the Compound Discoverer 3.2 software lists Material Order No., Product ID, and Description for various license types, including single license, multi-license, and upgrades from other Thermo Fisher Scientific software.

Continue with the relevant activation topic based on your computer's internet connectivity.

Activating the license on an online computer

Follow these instructions if your processing computer has an Internet connection.

1. If you have not already entered the licensing information, do so in the Activation Code view of the License Activation dialog box.
2. Click Online Activation to process the activation code.
3. At the confirmation prompt, click OK.
4. At the “new features” prompt, click OK. This completes the online license activation process.

Activating the license on an offline computer

Follow these instructions if your processing computer is not connected to the Internet. Activating the license on an offline computer is a three-step process requiring access to an online computer.

1. Create an activation request file (Activation-Activation Code.req) on the offline computer.
2. Transfer the activation request file to an online computer, upload it to the licensing portal, and obtain a response file (activation.xml).
3. Transfer the response file (activation.xml) back to the offline computer and process it by clicking Process Response File in the License Activation dialog box.

To activate the software license on an offline computer:

1. If you have not already entered the licensing information, do so in the Activation Code view of the License Activation dialog box.
2. In the License Activation dialog box, click Offline Activation. The Save Activation Request File dialog box opens.
3. Save the activation request file (Activation-Activation Code.req).

Figure 4: Offline activation instructions illustrates the process of saving the activation request file.

Click OK. The Activation Code view reappears.

Tip: When you close the Offline Activation dialog box, the application automatically saves the URL to the Clipboard for easy transfer to an online computer.

(Optional) Save the URL to a file.

Keep the License Activation dialog box open on the offline computer. If accidentally closed, restart the process from step 1.

To download the response file (activation.xml) from the licensing server (on an online computer):

1. Transfer the activation request file (Activation-Activation Code.req) to the online computer.
2. Go to the following URL (case sensitive): https://thermo.flexnetoperations.com/control/thmo/offlineActivation. The Life Sciences Mass Spectrometry Software Download and Licensing Portal will open.
3. Click Choose File or Browse, select the request file (Activation Activation Code.req), click Open, and then click Process. The server downloads the activation file.

Figure 5: Software licensing portal with a view of a downloaded response file shows the portal interface for processing the request file.

Save the response file (activation.xml).

To activate the license on the offline computer:

1. Transfer the response file (activation.xml) to this computer.
2. In the License Activation dialog box, click Process Response File. The Open Response File dialog box opens.
3. Browse to and select the response file (activation.xml), then click Open.
4. At the “license response processed” prompt, click OK.
5. At the “new features” prompt, click OK.

This completes the offline license activation process. The License Manager will indicate that the license for the specified product is permanent.

Trademarks

Compound Discoverer and mzCloud are trademarks of Thermo Fisher Scientific Inc. in the United States.