To open a Database Manager window, choose one of these options:

• Click on the Database Manager  button on the tool bar in the main window or choose the Tools | Database Manager menu item - an empty Database Manager window will be opened.
  
  
• Or open one or more mass spectra from a file, by choosing the File | Open | Mass Spectrum menu item and the spectra will be loaded into Database Manager.
  
  
• Or start any search from the Search menu and, if a spectrum or structure is found, a Database Manager window will be opened containing search results.

Spectral tree and structure panes are detachable windows that can be dragged and placed anywhere inside or outside of a Database Manager window. In addition, these windows can be switched on or off using the module buttons  ,  . This is a useful feature if, for example, you are dealing with single stage spectra (not MS/MS) and do not need a tree pane on your desktop.

In addition to the mass spectrum or spectral tree and the chemical structure, each record can include number of compound identifications, property and origin information. This additional information, which is associated with the record, can be found in the Info page in the Database Manager window. The Info page contains editable fields organized by group and subgroups. Fields holding information that is automatically calculated from a chemical structure (formula, mol. mass, etc.) or acquisition settings adopted from a file cannot be edited. Text in non-editable fields is grayed. The information in the Info page is divided into three groups:

The predefined list of additional information associated with a record may contain a large number of items that may be largely unused, Mass Frontier allows items to be selected which will appear in the Info page for each library separately.

To exclude or include items from the predefined list of additional information, follow these steps:

• Click on the Layout button  in the Database Manager window and select the Info Grid Layout pop-up menu item. The Info Grid Layout dialog window will open.

The Compare Spectra tab in Database Manager allows you to compare two spectra. The bottom spectrum is from the active record in Spreadsheet. The middle spectrum displays the difference between the top and bottom spectrum. The top spectrum can be added from an active record by pressing the Add button or can be pasted from the Clipboard by pressing the Paste button. The peaks in the top and bottom spectrum have different colors, thus the color of a difference peak in the middle spectrum is taken from the spectrum that has a more abundant peak at a particular m/z value.

To open mass spectra from a file:

1. Click on the Open  button in the Database Manager window and select Open Mass Spectra from popup menu item, or choose the File | Open | Spectra menu item.
   
   
2. Select the appropriate data format in the Files of type: combo box.
   
   
3. Select the file you want to open and click OK.

To save one or more spectra from Database Manager:

1. Select record(s) that contain(s) spectrum(spectra) you want to save.
   
   
2. Click on the Save  button in the Database Manager window and select Save Mass Spectra from popup menu item, or choose the File | Save | Spectra menu item.
   
   
3. Select spectra data format in the Files of type: combo box.
   
   
4. Type name and click OK.

Mass Frontier supports three file formats for spectra: JCAMP, MSP and Xcalibur® RAW format. The firs two formats are ACSII files. Structures can be opened and saved in MOL-format. Database Manager provides the possibility to save and open references to spectra that are contained in a library or external files. When saving references to a file, the spectra will not be physically stored, instead only information about the spectra location will be saved. For example, this allows you to save library search results as references to records in library. You may also wish to save groups of spectra as references, which thereafter are submitted for classification using the Spectra Classifier and Spectra Projector modules. The reference files are ASCII files with a *.ref extension.

To select more then one record in Database Manager Window, choose one of the following:

• Click on the first record you want to select and then click on the last record while holding the SHIFT key.
  
  
• Or point the mouse arrow at the first record you want to select, press the left mouse button, move the mouse pointer to the last record while holding the mouse button and finally release the left mouse button.

Note: You cannot select multiple noncontiguous items using CTRL key.

Records (spectra, trees, chromatograms) can be copied or moved from one Database Manager window to another by using the cut, copy and paste functions. Records can also be copied or moved to different locations within a spreadsheet in the same Database Manager window. This permits clear organization and maintenance of your experimental data or search results.

You can export four types of data from Database Manager to Microsoft Excel: text tables, graphics, mass spectra in numerical table format and spectral trees. Because all these types can be accessed at the same time, you must specify the type of data you want to move to Excel.

Mass spectra in table format or spectral trees stored in Excel can be imported to Database Manager via the Clipboard. Spectral tables can be organized horizontally or vertically. In order to correctly interpret m/z values and abundance you should follow one of these conventions:

Chemical structures are used at every stage in the Database Manager module and can be easily added to corresponding record. A particularly useful feature of Mass Frontier is its ability to create user libraries with structures including isotopes, ions, radicals and optically active compounds. Structures in Database Manager can be used in connection with the Fragments & Mechanism module to check the consistency of a mass spectrum and chemical structure. Database Manager allows you to perform structure elucidation through modification of input structure and regeneration of product fragments.

You can copy a structure you wish to paste into Database Manager, from anywhere in the program. To paste a structure into Database Manager, use the Paste Structure button in the top right corner. The Copy and Paste buttons on the button bar are intended for records, not for single structures.

Structures can be imported to Database Manager by loading them from an external MOL-file or SDF-file. In contrast to the pasting of a structure, when you load from an external file you can add structures to more than one record at a time. This allows you, for example, to assign a large number of structures to library spectra when importing an external library to Mass Frontier.

Chemical structures can be added not only to a spectrum or tree node but also to any peak. To add a chemical structure to a peak, click the Assign Structure to Any Peak button  in the Database Manager tool bar. A New Structure Editor will open and you can draw a fragment. After you finish drawing, the program will automatically attempt to connect your structure with a spectral peak according to the fragment's m/z value. If, for whatever reason, you need to connect the drawn fragment to a different peak, simply drag the connecting circle with the mouse to the required peak. The drawn fragment can be resized. Fragments generated by Fragments & Mechanisms window can be assigned automatically to peaks in a spectrum

Mass Frontier allows the automated prediction of fragments from a user provided structure. If you start the generation of fragments from Database Manager and the active record contains a structure (an MS1 structure for Spectral Tree), the generated fragments are automatically linked with peaks in the spectrum (spectra in the Spectral Tree) according to their m/z values. After a generation, highlighted (“explained“) peaks are displayed in a different color (in red by default) in the original mass spectrum. Clicking on a highlighted peak reveals all the mechanisms leading to it. In addition, generated fragments (a corresponding Fragments & Mechanisms window must be open) can be assigned automatically to peaks in a spectrum by clicking on the Spectrum Processing button   and choosing the Auto Fragment Annotation of Peaks pop-up menu item.

Database Manager serves as a gateway for several modules. Mass spectra can be imported directly from a file, Chromatographic Processor, Microsoft Excel®, or Xcalibur®. They can also be exchanged between Database Manager modules. In addition Mass Frontier is able to automatically establish a link between Database Manager records and other modules that need to access spectral or structural data. The ability to link equivalent spectral information allows you to access the original data that was supplied as input information for one of the many interpretation methods available in Mass Frontier. The direct feedback between source (records and mass spectra) and results (mechanisms, bar code spectra, classes and projections) is particularly useful as it helps you keep track of all the modules that originate from a single source. This feature makes it easier to employ more modules simultaneously allowing more sophisticated problem solving approaches.

The Spreadsheet is organized on a row basis. Each record is represented by a single row. The columns contain supplementary record information. In the spreadsheet you can move columns by dragging the appropriate column header to a new position. If you want to move a row, use the cut and paste functions as dragging rows is not supported.

When you open a Database Manager window, the spreadsheet will be empty. You can add records to it by conducting a search, opening spectra or references, or by pasting records or standalone spectra. For an active record the associated spectrum or tree, and structure (optional), appear in the upper half of the window. The hand cursor in the first column indicates which record is active. You can select more then one record, but the row with the hand icon is always the active one.

To export a data reduced chromatogram to Database Manager, select the desired scans or components in Chromatogram Processor and use the copy and paste commands. To select multiple scans or components, use the Shift or Ctrl keys. Data reduced chromatograms present in Database Manager can be saved to any library using the same procedure as for saving spectra or trees. Components from data reduced chromatograms can be edited or searched in Components Editor that can be opened using Edit Components    button. Chromatographic scans or trees are fully searchable, if the search option is enabled (Library Search window, Advance page, Search In group box):

For retrieving spectra, trees, chromatograms and structures from libraries, several query and search features are available. Mass Frontier allows you to search every library simultaneously. The following search options are available:

• Spectrum Search - searches for the library spectra most closely matching an unknown spectrum.
  
  
• Tree Search - searches for the library spectral tree most closely matching an unknown spectral tree or subtree.

Mass Frontier uses search algorithms developed by HighChem and NIST. These algorithms are based on the optimized dot-product function together with an additional term, based on ratios of peak intensities.

A structure or substructure query can be taken from Structure Editor, Database Manager or a fragment copied in Fragments & Mechanism window.

Structure and substructure searches are very important features for retrieving library entries. The structure search is the most straightforward method for finding compounds in a library. Since the rules of systematic nomenclature need not necessarily lead to a unique name for each compound, name search can be, in many cases, very ineffective. It is much easier to draw or import a structure query than to type a complicated name. It is also more natural for a chemist to deal with structures rather than names or CAS numbers.

The name search option provides incremental search capabilities. As you start typing a portion of a name, a list of compounds that begin typed to this point will be displayed with slight delay. The chemical structure is displayed for the highlighted name. You can use up and down mouse keys to browse the displayed names. The library name search covers all three name types: IUPAC, Synonyms and Commercial Product.

Each library entry is individually numbered. In this mode you can search for a single ID number or for a range of ID numbers. The ID search dialog window contains two edit boxes to input the ID range: From and To boxes. If you want to retrieve a single ID number, the second box (To) can be left blank. The maximal ID number that can be found is displayed in the Max. ID box.

All searches, except Name Search, can be restricted by a set of constraints. The Dialog windows of these searches contain a panel with a radio button for activating constraints and a button for editing search constraints. When you press the Edit button a dialog box will appear that allows you to search selected libraries for matches with a set of specific criteria. Four constraint types are available: Molecular Mass range, Number of Atoms range, Allowed Elements and Good-Bad list. Searches conducted with activated constraints can be time consuming because each library entry is examined to find those that match the criteria you have set. The Search Constraints are especially useful when you are dealing with large libraries and you want to retrieve hits that are of interest for your specific problem.