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Mass Spec Calculator™ Professional

A Utility for Assistance in Mass Spectral Interpretation

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  • Draw chemical structures on screen quickly and easily
  • Fragment structures on screen using either manual or automated routines
  • Compare Predicted Fragmentations with Observed Mass Spectra
  • Instantly calculate & display isotopic profiles of molecules or fragment ions
  • Calculate possible elemental compositions for a given mass
  • Automatically digitize a graphical mass spectrum to a mass-intensity data file
  • All modules now support 79 elements, including essentially any element likely to be encountered in mass spectrometry.
  • All elemental data including mass, number of isotopes, and each isotope's mass and relative abundance can be easily edited if desired.
  • MS Calc Pro automatically adjusts to the available screen resolution to maximize the drawing space;
    additional virtual screen space can be accessed by activating scrollbars.
  • The drawing routines have been improved, several new options have been added, a tool bar and pop-up menu are included
    for additional ease of use, and a new alkyl chain tool and a user-defined "R-group" tool have been added to further speed the drawing process.
  • MS Calc Pro includes an enhanced Isotopic Profile utility based on a completely new algorithm that provides essentially
    unrestricted analyses regardless of the number of polyisotopic atoms present in the structure.
  • Includes an enhanced Elemental Formula utility that supports all 79 elements and provides additional analysis and display features
  • Includes a new utility that can automatically digitize a scanned spectrum and import it for use within MS Calc Pro.
  • Includes improved spectrum and printing capabilities.

1. To begin using MS Calc Pro, one would generally first draw a structure. The MS Calc Pro drawing editor is designed to be very simple and easy to use, and a variety of preformed rings, functional groups and other structures are available to assist in this process. For example, the structure of nicotine can be drawn on screen in seconds in just six steps. This compound was drawn by placing two preformed rings on screen, then adding the bond, two N atoms and the methyl group as added objects.


2. The structure could be saved to disk, then converted to cotinine by adding =O in one step to form the lactam structure. The two structures shown here could thus be drawn and saved for later use by using just 7 steps and in less than 30 seconds.


3. Once a structure has been drawn, it can be analyzed in a number of ways. The most fundamental operation is manual fragmentation. This is done just as you would do using paper and pencil, but with electronic speed and accuracy. For example, to examine a homolytic break of the bond linking the two ring structures of nicotine, you would simply draw a line through the bond using the mouse; the program will instantly calculate and display the resulting two fragment masses. The display is color-coded to clearly link the fragment atoms with the associated mass.

This instant manual fragmentation process is interactive and can be repeated as often as desired. Manual fragmentation draws upon your knowledge of likely fragmentation routes to focus your time and effort on the most likely possibilities. There are three different manual fragmentation modes available including a 'free-form' option to accommodate any sort of fragmentation you might wish to examine. Multiple and sub-fragmentations of compounds can also be examined, and the display can be instantly switched between nominal and accurate mass resolution.

Auto-fragmentation results are only a mouse-click away. In the screen shown below, nicotine has been auto-fragmented by MSC and the user has selected mass 39 in the fragment list ... this automatically redraws the structure with the three atoms present in the fragment (C3H3) indicated on screen. This process of identifying specific fragments in the structure can be repeated as often as desired. These results can also be directly compared with the actual mass spectrum, either imported as an ASCII file or recreated within MSC; also, fragment isotope profiles can be instantly calculated and displayed; additional possible fragments including major rearrangement products such as McLafferty or tropylium ions can be identified; etc.


Once a molecule has been auto-fragmented, it can also be compared with an observed mass spectrum by choosing the 'Match' option button. This enables you to essentially overlay the projected and observed spectra, match predicted and observed isotopic profiles for the molecular ion, and calculate an overall 'Match Index' for the actual and predicted spectra.

MSC also includes utilities for determining Isotopic Profiles, for calculating possible elemental compositions given a mass, and for importing user spectral data in a variety of text formats, or creating spectral files directly from data entered onto an internal 'spreadsheet'.

The screen below demonstrates the Isotopic Profile utility. The user has drawn the structure of dioxin (TCDD) and then clicked on the Isotopic Profile Speedbutton. MSC Pro automatically incorporated the elemental composition for the TCDD structure, carried out the calculations, and instantly displayed the window shown here displaying the theoretical profile in both text and bar graph form. Compositions can also be entered and edited directly, and additional options such as to display the results in accurate mass form are available.


MS Calc Pro includes an enhanced Elemental Composition utility. With this tool you can enter a mass and tolerance, select the elements to be considered (with additional constraints if desired such as to specify the range of an element to include; or only show possible molecular ions; only formulae adhering to the 'Nitrogen Rule', etc.), and then click on the 'Calculate' button to have MSC calculate all possible elemental compositions fitting those conditions.

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