Mass Spectrometry Data center
Written by Meng Zhai
Chemical and Biochemical Reference Data Division
National Institute of Standards and Technology (NIST), Gaithersburg, Maryland
For inquiries regarding this program please contact Dr. David Sparkman at email@example.com.
Download the program here (1/8/2010).
The following is a tutorial on how to digitize a mass spectrum using the NIST Mass Spectrum Digitizer Program. These are step-by-step instructions on how to go from a graphic image to an .msp file containing the desired information. The NIST MS Search Program can then import the .msp file.
This program requires that Oracle’s Java be installed (https://java.com/en/). Click on the Free Java Download button.
Oracle’s Java is already installed on many computers. Download the NIST Spectrum Digitizer Program. This file (SpectrumProgram.jar) will be in the \Download folder. When the Mouse pointer is put on the Program’s name and the left Mouse button is double-clicked, the Program will run, if Java is installed. If the Program causes a dialog box to be opened that ask for an association, it will be necessary to first download and install Java. After Java has been installed, try to run the Digitizing Program again.
There is no installation and no icon is created for the Digitizing Program. For convenience, it may be desirable to move the Program to the folder containing the NIST Library, e.g., \NIST17. It may also be convenient to create a Desktop icon, but the Digitizing Program can always be started from Windows Explorer by putting the Mouse pointer on the name and double-clicking the left Mouse button.
When a graphic spectrum is imported it may include numeric labels on the X-axis (abscissa) and the Y axis (ordinate) and the tops of some of the peaks. The spectrum may have a graphic representation of a structure. None of these annotations are taken into consideration by the Program in the digitizing process.
When a graphic spectrum is displayed in the Program, it cannot be Closed. Opening a new graphic display will replace the existing display, clear the Points List (lower part of the Vertical Information Column on the right side of the Program’s desktop), the X Calibration Points List, and any zoom from the previous display. The spectrum information fields (text boxes at the top of the display) are not cleared when a new spectrum is displayed. It is necessary to put the Mouse pointer on the Clear button (one of four buttons on the left side of the top of the desktop, in line with the text boxes) and click the left Mouse button to clear these fields. The Date: and Digitizer: fields will not be cleared when the Clear button is selected. The Date: field updates automatically. Whatever is in the Digitizer: field remains until changed, even when the Program is closed and re-opened.
The Y0: and Y1: fields ARE CLEARED when a new graphics display is opened. The Left and Right positions and the Threshold positions ARE NOT CLEARED. It is best to reset these three positions for each new graphic.
When the Digitizing Program is closed by putting the Mouse button on the X button at the far upper right of the desktop and clicking the left Mouse button, all data is removed. When the Program is started at a later time, the previous data and information will be gone. Only the Date: and Digitizer: fields will be populated. The default File Open dialog box and the default File Save dialog box will point to the folders last used before the Program was last closed.
When the Mouse pointer is placed on the upper Reset button (previously, the Done button) in the upper part of the Vertical Information Column on the right side of the Program’s desktop, and the left Mouse button is clicked, all the values in the X Calibration Points List will be cleared and all the Digitized m/z – intensity Pairs List will be cleared. The affected zoom will remain. The values for Y0, Y1, Left, Right, and Threshold will be retained. The label on this Reset button returns to Done.
When the Mouse Pointer is placed on the lower Reset button (previously, the Set Points button) and the left Mouse button is clicked, only the Digitized m/z value-intensity Pairs are deleted. The label on this button then returns to Set Points. The Y0 and Y1 values, Left, Right, and Threshold values and the X Calibration Points are not cleared. It is now possible to alter these various parameters to achieve a better digitization.
Figure 1. The NIST Mass Spectrum Digitizer Program Desktop. The vertical red line is used to fix the position of the X points and the Left and Right Boundaries which are indicated by the two vertical-green lines on either side of the spectrum. The horizontal red line is used to fix the Y0 (base line of the mass spectrum) and Y1 (maximum intensity) points and the Threshold, which is indicated by the horizontal turquoise line.
The Program will always open with no data loaded. A blank desktop.
Information about the molecule/spectrum can be entered in textboxes at the top of the Program’s display. Put the Mouse pointer in the box where information is to be added and click the left Mouse button. Type the desired information. Press the Enter key or move the Mouse pointer to another box. It is best to use the Clear button to clear these fields before starting to add new data.
To view the contents of the .msp file, open it with Notepad.
Note: Shortcut keys can only be used if a textbox is not selected. To deselect, click anywhere on the image or the black space.
Spectrum Digitizer Program will warn about error with pop-up window similar to this:
Description of possible errors is following.
1. Invalid calibration input.
An integer for one of the calibration inputs (Image/Real X, Y0, Y1) was not entered. No decimals, letters, other characters, etc. are allowed.
2. Boundaries out of bounds.
One of the boundary lines is out of bounds. One of the following is happening:
3. At least two X values required.
As many X calibration values as wanted can be entered, but there needs to be at least two unique ones.
4. Calibration points repeated.
There cannot be repeated calibration points. At least two unique calibration values for X must be entered.
5. Please remove duplicate.
The final list of x, y values that is save is not allowed to have pairs that share the same X value. Delete or change the duplicate pairs at the X value shown.