Files can be opened in the usual manner. Clicking on the Open File button will display a 'file' list box that displays only directories. Navigate through the tree structure to locate your file of interest. The selected drive can be changed from the drop down list above the display. Any Agilent Mass Hunter or Chemstation file should be listed with the standard .D extension. Double-clicking on that file will open the file and display the total ion current chromatogram. The file contents (scan number, retention time and abundance) are displayed in the box on the right side of the screen. The number of scans in the current file is shown in a small box at the top left of the screen, and the file name and type are displayed. If the file contains time of flight data then that will be indicated in the Type information with a reminder that spectra are not available for high-resolution files.
The "file" display is actually of directories which is how Agilent files are stored. Quadfiles opens files by examining the contents of every directory with a .D extension, determining if it is Chemstation, Mass Hunter, or non-Agilent related, and opens the appropriate file if possible. Since this operation occurs only on a directory change event, if you want to close and then reopen a file you cannot do so by simply clicking on the same, current directory. You will need to change to a preceding or subsequent directory and then click back to initiate the directory change event and open the file within it.
The TIC can be zoomed as needed by left clicking and holding in the Total Ion Current window, and drawing a box around the region of interest. The number of scans selected and the extent of scaling will be determined by the dimensions of the box when the button is released. This can be repeated as needed. To restore the full display, left click anywhere in the plot.
If the file contains low resolution data such as a Single Quadrupole MS1 Scan then that will be indicated in the Type heading. With these data you can right-click on any peak (or any point) to display the mass spectrum for that scan. This will be displayed in the default format of TIC in the top window and the current spectrum in the bottom. The present scan number is displayed in the Spectrum window heading and also highlighted in the mass-intensity list. When a spectrum is selected, the number of ions and the base peak in the spectrum will be displayed beneath the Scan number box. If the contents are SRM or MRM then the parent ion also will be displayed for the current spectrum.
The spectrum can be zoomed and restored in the same manner as the TIC using the left mouse button. If you draw a selection region in the spectrum window by using the right mouse button, then the included spectra will be averaged and displayed, and the Spectrum window heading will indicate a scan range. Display of the TIC full scale, the spectrum full scale, or the combined display can be switched at will by clicking one of the buttons to the top right of the display. The TIC and the Spectrum can be printed if desired by selecting that option under the File menu, and each can be copied by selections on the Edit menu. The images are copied as Windows enhanced metafiles and can be pasted in any usual target such as Word. Since they are metafiles and not bitmaps, the images can also be further edited within Word or other destination document.
