Mass Frontier library utilities are based on the Microsoft SQL Server 2000 Desktop Engine (MSDE 2000)®. MSDE 2000 is a data engine built and based on core SQL server technology. It is a reliable storage engine and query processor for desktop applications. MSDE 2000 is a royalty-free, redistributable database engine that is fully compatible with the SQL Server. MSDE 2000 is included in the Mass Frontier installation process.

Mass Frontier can work either as a standalone application, or can be combined with the NIST/EPA/NIH Mass Spectral Database 2002 (NIST 2002 Library). If the NIST 2002 Library has not been simultaneously installed with Mass Frontier, the library can be either installed, if the library is in Mass Frontier format, or imported from NIST file format. During import of NIST library the data will be converted to Mass Frontier database format (SQL Server) . This process can take several hours. If you select NIST Main library the NIST Replicate library will be automatically installed. NIST Replicate library cannot be installed as a standalone library without the Main library.

At HighChem, we have been collating spectral trees (MSⁿ spectra) for a number of years and these are available in Mass Frontier. This unique collection contains high quality ion trap spectra of human and veterinary pharmaceuticals, endogenous metabolites, drugs of abuse and doping agents. The library contains spectral trees acquired by electrospray ionization (ESI) in both the positive and negative ion mode. Each spectral tree contain name, structure and CAS number. HighChem Spectral Tree Libarry™ currently contains more than 7.000 individual spectra of 1041 positive and 524 negative ESI spectral trees.

To install a user, NIST or HighChem Spectral Tree Libraries™ into Mass Frontier, choose the Library | Spectral Library | Install Library item from the main menu. When the Install Library dialog window appears, follow these installation steps:

Experimental data, as well as reference spectra, can be stored in user libraries. It is very easy to create a user library, so don’t hesitate to organize your mass spectral, chromatographic and structural data in user libraries. Mass Frontier allows you to create highly annotated user libraries with structures. Both low- and high-resolution mass spectra are supported. Mass spectra can be stored as individual single spectra or as MSⁿ trees with multiple node spectra. Data reduced chromatograms with selected scans or components can be stored in user libraries and searched.

Since database files can be copied or deleted only if the library is uninstalled, you may need to uninstall a library. In addition, a high number of libraries can slow the overall performance of Mass Frontier so the uninstallation of unused libraries can be of benefit. If you uninstall a library, the library is not deleted. The library reference is merely removed from the program without the loss of spectral or structural information. An uninstalled library can be reinstalled at any time. Mass Frontier allows you to install or uninstall a library as many times as you wish.

Mass Frontier provides a simple way of adding new records (spectra, trees, chromatograms, structures and compound identification information) to a user library. This option creates new library entry with new ID. If you just want to update an existing record you have to use Save Changes in Library option.

Any record information (spectra, trees, chromatograms, structures and compound identification information) can be changed and saved in library. If anything is changed in the record a small circle is displayed in Database Manager in the ID Num. column in the spreadsheet. Changes in records are not automatically updated in database unless you save them.

To save changes in library please choose Library | Spectral Library | Save Changes in Library in main menu item.

If you try to save a newly created record, you will be redirected to the Add New Records to Library option.

Deleting a library record will cause the information to be irreversibly lost. There is no undo function for deleted library records. You cannot delete library entries from NIST library.

If you want to delete one or more records:

1. Retrieve the record(s) you want to delete using any search.

2. Select the record(s) you want to delete in the Database Manager Spreadsheet.

3. Choose the Library | Delete item from the Library menu.

4. When the Delete From Library window appears, review the spectra and structures carefully.

5. If you want to delete all records at once that are displayed in Preview, choose the Delete without confirmation radio button. If you want to delete record by record, select the Confirm Each Spectra/Structure Pair Before Deletion radio button.

6. Press the Delete button.

A unique feature of Mass Frontier is the ability to create searchable libraries of data reduced chromatographic data. Retention times and TIC profiles, as well as selected scans or detected component spectra or trees can be exported to user libraries and searched using various criteria. This feature allows you to search a particular spectrum in a series of GC/LC/MSn library records (target analysis), or you can perform cross matching of all scans or components in a chromatogram against spectral data of other chromatographic records (dereplication). Chromatograms are organized in a similar manner to spectral libraries, with the difference that a single library entry represents a data reduced chromatogram rather than a simple spectrum or tree. A data reduced chromatogram can contain up to 999 individual scans (spectra), or 999 detected components (spectra or trees).

To open the SQL Server & Library Tools dialog window, choose Library | Library Tools from the main menu tool bar. The SQL Server & Library Tools dialog window contains three tabs:

• Spectral Libraries

• Fragmentation Libraries

• SQL Server

Spectral Libraries

The Info grid lists all the attached spectral and chromatographic libraries to the SQL Server. Libraries incompatible with the current version of Mass Frontier can be detached or removed from your system via the context menu (right mouse click).

In the Update group, you can Compress or Reindex selected libraries to shrink their sizes, or defragment indexes if the performance decreases. Please be aware that these actions may require some time to perform, depending on the amount of stored data.

Fragmentation Libraries

The Info grid lists all the attached spectral and chromatographic libraries to the SQL Server. Libraries incompatible with the current version of Mass Frontier can be detached or removed from your system via the context menu (right mouse click).

In the Update group, you can Compress or Reindex selected fragmentation libraries to shrink their sizes, or defragment indexes if the performance decreases. Please be aware that these actions may require some time to perform, depending on the amount of stored data. If you build large fragmentation libraries, these actions should be performed regularly.

SQL Server

The Monitor group box displays information about the SQL Server status and contains buttons for starting, running and stopping the SQL Server service.

The Extended Stored Procedures check box in the Reload group box allows you to redefine the extended stored procedures used by the SQL Server. These procedures are essential for spectra search functionality. Use this action if a library search does not work properly.

The Default Library check box in the Reload group box will recreate damaged internal database files. Use this action if the message ”Cannot open library DefMSMSLibrary!” appears.

The Connected Libraries check box in the Reload group box will reconnect all the spectral libraries. Use this action if the SQL Server was stopped and restarted outside of Mass Frontier, for example, in the task bar notification area (SQL Server Service Manager).

It is not advisable to perform backup and restore of spectral or fragmentation libraries by a simple library files copy and paste operation. We recommend you use the safe backup and restore procedure in Mass Frontier.

To backup a library, follow these steps:

1. Open the SQL Server & Library Tools dialog window by choosing the Library | Library Tools main menu item

2. Select the library type by clicking on the Spectral Library or the Fragmentation Library tab

3. Click on the Backup/Restore button and the dialog window will open

4. Specify the library you wish to backup and enter the Name, Description and Destination of the backup files

Library data can be restored from previous backups into a new library or into an existing library.

To restore a library from backup files, follow these steps:

1. Open the SQL Server & Library Tools dialog window by selecting the Library | Library Tools main menu item

2. Select the library type by clicking on the Spectral Library or the Fragmentation Library tab

3. Click on the Backup/Restore button and the dialog window will open

4. Specify the library name in the Library to Backup combo box where the data is to be restored. Please note that you can enter a new library name here.

5. Select the library data you wish to restore from the list of backups