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Category: MSD ChemStation / Data Analysis

Records returned: 16

MSD ChemStation / Data Analysis

1. Using GC/MS MSD ChemStation I want to display mass chromatograms and a TIC overlaid on one another with the TIC normalized to 100% and the highest mass chromatographic peak also being set to 100%. (id=2)

The MSDChem Station software allows for the display of a TIC and reconstructed ion chromatograms (RIC ? the same as a mass chromatogram) at the same time. This is done with an option from the Chromatogram menu of the Enhanced Quantitation mode of Data Analysis. You have to first specify that the chromatograms are to be displayed overlaid. This Display of Overlaid chromatograms is call the Merged Format. This Chromatogram menu option is a toggle and remains set as long as you are using Data Analysis. If you exit and restart Data Analysis, you have to set the toggle to the Merged Format.

The Merged Format, normalizes the display to the largest peak. You cannot set the display to normalize the TIC and separately normalize the RICs. It may be possible to create a macro to do this. You can zoom the display to make the RIC peak more visible, but this will cause the TIC peaks to go off scale. It may be possible to create a macro to do what you want. This is a good question to Ask Dr. ChemUser.

2. Using the GC/MS ChemStation I want to have a spectrum number appear on the tail of the Mouse pointer as I drag accross the TIC (id=4)

There is no know way to do this. This ability will require custom programing. Ask Dr. ChemUser how to go about contracting for this feature.

3. I would like to display two spectra at the same time I am looking at a chromatogram in the GC/MS MSD ChemStation. (id=7)

I have done this with the use of two macros and a modification to the enhmsbar.mac that is in the \MSDChem\MSEXE directory.

BEFORE YOU MODIFIED ANY MACRO, MAKE A BACKUP OF THE MACRO YOU INTEND TO AND STORE IT IN A SAFE PLACE!!!!!

The following modifications are made to the enhmsbar.mac file. Open the file in a text editor such as NotePad. Do a search for the word Chromatogram. This will take you to a line that reads:

MENUNEW "&Chromatogram"

Menucmd "Select C&hromatogram Labels...","enh_chromlabels","Allows selection of Peak Labels"

menusep
    MENUCMD "Tile &Two Spectra","macro _exepath$+""tile"",go","Displays Chromatogram, Spec in X, and Spec. in Y."
    MENUCMD "Tile &One Spectrum","macro _exepath$+""tile2"",go","Displays Chromatogram and Spectrum in X"
menusep

Create the two macros (tile.mac and tile2.mac) using NotePad. When you save these two files, be carful that they DO NOT have the extension .TXT. NotePad will save all files with the extension .TXT. If you have not set your view in Windows Explorer to deselect the option of "hide extensions of known file types", you will not see the .TXT extension. To make sure the .TXT extension is not present, use the rename function in Windows Explorer to view the file name and it extension.

Contents of Tile.MAC

name tile
R9 = Y
Draw 3, R9
Window 2,0:1,.5:1
Window 1,0:.5,0:.5
Window 3,.5:1,0:.5

name tile2
Window 2,0:1,.5:1
Window 1,0:1,0:.5

After several spectra have been displayed in the X Register display (display on left) the right spectrum window will close. Use ether of the options on the Chromatogram Window to restore the lower part of the display.

4. In the GC/MS MSD ChemStation after I have expanded a TIC to a range, I would like for this to be the default range when I select m/z values for mass chromatograms or ask for a merged format display. (id=8)

There is no known documented way to do this. This will require a custom macro the is a good question to,Ask Dr. ChemUser.

5. Often, I have the need to reprocess large amounts of data with my GC/MS MSD ChemStation. Is there an easier way to do this without re-processing the complete method? (id=13)

Yes. There are many tools within the Productivity MSD ChemStation that enhance the process for automated batch processing. A few of these tools are: DoList, DoScan and Qedit.? DoList, will allow you to reprocess a batch of sample data much the same as the initial processing. To request more specific information please send a request to,Ask Dr. ChemUser.

6. I am using G1701AA Version A.03.02 and G1701CA Version C.00.00 on a computer that has Windows 95 operating system. I cannot upgrade to a later version of the GC/MS MSD ChemStation because I have the IRD and the later versions do not control this detector. My screen resolution is 1024 by 768. When I display a spectrum or chromatogram, the numbers on the y-axis (abundance scale go off the left edge of the screen. The only thing visible for large numbers is a string of zeros. I found that by entering FontAxis = "gevena, 6,0,0" in the Command Line at the bottom of the display I can change the font to where all the numbers are visible on the y-axis. I want this change to be permint so that when I exit Data Analysis and return that the correct font is installed. (id=42)

Close the GC/MSD ChemStation Data Analysis. After making a backup copy of ENVINT.MAC, open the macro ENVINT.MAC in the hpchem\msexe with Notepad. Select Search from Notpads Menu bar. Select Find from the Search menu. Enter the string fontaxis in the text entry box of Find dialog box and click on the Find Next button. This will take you to an area of text that contains the following: PLOTFONT = "" FONTTITLE = "" FONTANN = "" FONTAXIS = ""

Change: FONTAXIS = ""

7. Every time I open one of my data files using Data Analysis in the GC/MS MSD ChemStation, the TIC and two weird-harold chromatograms are displayed. Theses chromatograms have regularly displayed peaks. I have to close them and then resize them. When I look in the data file folder, I see two files TST1A.CH and TST2A.CH. If I delete these two files the data file will not open. I do not want to look at these chromatograms. What are they? (id=49)

Somehow in your acquisition method you have requested that two additional channels of data be acquired. The CH extention on the file is the indication that a 2-D GC data file is being created. This is what happens when you are simultaneously acquiring data from an FID or other conventional GC detector while acquiring mass spectra or a separate TIC while acquiring mass spectral data.

The data files you have already acquire have these separate channel files associated. There is no way to remove them. However, you do not have to look at them.

1. Open the File
2. Select the File Menu
3. Select the Select Signals option. If there are no separate signal files, this option is grayed.
4. The Select Signal to Load dialog box is displayed. The top entry is Data MS, the other entries are for the other data channel files. All the check boxed have a check mar in them.
5. Deselect the items you do not want to display when the file is opened.
6. Click on the OK button
7. The deselected item will no longer be displayed and each time you open the file they will not be displayed. Only the select chromatogram will be displayed on file open.

You can keep these unwanted files from being created in the future by looking at the acquisition method. Look at the DETECTORS portion of the method. It appears that you have activated the Test Plot chromatogram feature in the method and are saving these test plots along with the mass spectral data.

Select Edit the acquisition method and go to DETECTORS, check to see if CHANNEL A (1) and CHANNEL B (2) data are being saved. If they are, deselect these items. The DETECTORS section in a GC/MS method is not normally utilized and this section is for setting up 2-D detectors, a.k.a. FID, TCD, Test Plot.

8. How can I place total ion chromatograms (TIC) and extracted ion chromatograms (EIC) into a WORD document? (id=107)

First, load in a data file in the Data Analysis view of your MSD software. You should see that window number 2 contains the TIC. At the command line type "clip 2", then press the enter key on your keyboard. Clip sent the chromatogram into the WINDOWS clipboard. Next, open WORD and place the cursor where you need the TIC to appear. Press both the Ctrl and V keys at the same time, and you should see the TIC appear in your WORD document. Next, go back to your MSD Data Analysis software. Use the Ion Chromatogram menu item to draw an ion chromatogram. Again, window 2 should contain it. Again, type "Clip 2" at the command line, then go to WORD and press Ctrl and V at the same time. You should see the EIC in WORD.

9. Why are there underlines under specific letters of the selections on the Menu Bar? (id=93)

If you hold down the Alt key and press one of these underlined letters, that Main Menu Bar selection?s menu will be displayed. If you press a letter that is underlined for one of that menu?s selections, the specified function will be carried out.

10. After selecting a spectrum in the GC/MS MSD ChemStation Enhanced Quantitation mode using the Right Mouse button, I want to be able to look at the spectra on either side without having to try an pick them using the Mouse pointer. (id=94)

Under the Spectrum menu in the enhmsbar.mac file there are two commented-out commands, Previous and Next. You can remove the ! in front of these two lines and the commands will be functional. Before you edit any ChemStation system macros, make sue you have made a backup.

11. I was looking at the spectra of tribromobenzene (C₆H₃Br₃ (MW 312) and docosane C₂₂H₄₆ (MW 310) in the tabular display. The molecular ion peak for docosane was at m/z310.45 and for tribromobenzene was atm/z311.75. In the graphic display of these two spectra, the molecular ion peaks were labeled 310 and 312. Why is there a difference? (id=95)

The differences are due to the "mass defect" of the atoms that composes each of these molecular ions. The mass defect of an atom is the difference in the mass number (A ? the total number of neutrons and protons in the nuclease) of an atom and its exact mass measured relative to an atom of ¹²C. The ¹²C was agreed to by chemists and physicists, separately, in 1962. Hydrogen has a positive mass defect of 0.0078 and bromine has a negative mass defect of 0.0817. By definition, carbon has no mass defect.

When the m/z of the MSD is calibrated, the ions produced by the electron ionization (EI) of perfluorotributylamine are used. One of the reasons that this compound is used in the calibration of the m/z scale is because the mass defect of fluorine (0.0016) relative to its mass number (19) is very small. This means that even for the largest observed ion in the mass spectrum of this compound (614), the mass defect would be only 0.0353. This mass defect value will decrease for each subsequently smaller value used in the calibration of the MSD?s m/z scale. Therefore, the integer mass of each of the ions used to calibrate the scale is considered to be the same as its exact mass within the limits of the instrument. The MSD will report the m/z value of an observed ion to the nearest 0.05.

Tribromobenzene has a negative mass defect of 0.2215 due to bromine?s mass defect and the number of Br atoms in the molecule (3). Docosane has a positive mass defect of 0.3400 due to the mass defect of hydrogen and the number of hydrogen atoms in the molecule (46). The ChemStation rounds numbers between -0.3 and +0.7 to the nearest integer for graphical display and mass spectral database searches. There, 310.45 is rounded to 310 and 311.75 is rounded to 312.

12. What is a mass chromatogram? (id=96)

A mass chromatogram is a plot of the ion current of individual m/z value, a range of m/z values, or the sum of several discontinuedm/z values versus spectrum number for data acquired as a function of a chromatographic process. Some data systems, like the ChemStation, call mass chromatograms extracted ion chromatograms (EIC). There is no abbreviation or acronym for mass chromatogram. The chromatograms constructed from the sum of the ion currents of all the ions in each spectrum are sometimes called total ion chromatograms (TIC). The correct term for TIC data is reconstructed total ion current (RTIC) chromatogram. The plot of the ion current of individual m/z value, a range of m/z values, or the sum of several discontinuedm/z values versus spectrum number for data acquired through the direct infusion or the flow injection of a sample in LC/MS or the use of a direct insertion probe in GC/MS is called an extracted ion profile (EIP) or mass profile. Mass chromatograms should not be confused with selected ion monitoring (SIM) chromatograms, which result from the plot of ion currents of ions monitored during an SIM acquisition.

13. While in the Enhanced Quantitation Data Analysis of the GC/MS MSD ChemStation, I did something to get a very strange display. This display had what appeared to be two overlaid RICs covering the top half of the display. The bottom half had two Windows, one a little larger than the other. The larger one on the left had what appeared to an expanded view of the TIC for the same region as the RICs above. The Window on the right only had text: Peak 1; Retention time 4.17; and some other stuff. The Menu Bar only had three items: PkPurity, Spectrum, and Help. When I doubled clicked on the Right Mouse Button on either chromatogram, the lower left display was changed to a spectrum. I could not change the upper display. The only way I could get back to the regular data analysis was to reboot the computer. (id=102)

Somehow you got the Peak Purity View. This view is a result of selecting the View menu and then selecting the Review Peak Purity. It is best to never reboot the computer unless absolutely necessary. The way you return to the normal data analysis view from the Peak Purity View is to select PKPurity on the Menu Bar and then select Return to DA.

14. Often I have peaks in my mass spectra that don?t appear to make sense. How can I tell if a mass spectral peak belongs in a particular spectrum? (id=103)

Mass spectral sources can come from a lot of sources other than the analyte you are trying to identify (i.e., column bleed, matrix contaminants, instrument contaminants, etc.). The best way to determine if a particular mass spectral peak belongs with any other particular mass spectral peak is plot mass chromatograms for the m/z values of the peaks. If the resulting mass chromatograms rise and fall together with the same general shape, then the mass spectral peaks are from the same source. Often you will see that one mass chromatogram produces a chromatographic peak while the other produces a wavy line offset from zero. This is a good indicator the second m/z value is due to background. Some common GC/MS background ions are observed at m/z 207, 281, 355 (column bleed); m/z 149 due to the electron ionization of esters of phthalic acid that are often used as palletizes; and an ion series with the highest m/z value in each series being 29, 43, 57, and 71 arising from aliphatic hydrocarbons.

15. What is the main difference between the RTE and the Chemstation integrator? (id=106)

There are two integrators that you can use with the MSD Chemstation. One is the "RTE" integrator, and the other is the "Chemstation" integrator. The RTE is named that way because it is similar to the integrator from another data system that Hewlett Packard or Agilent used to sell called the RTE Data System. It was written to integrate mass chromatograms. It does NOT have timed events. Users who need timed events may prefer to use the Chemstation integrator. Timed events allow you to control integration on a time basis, such as turning the integrator ON at 2.0 minutes and then OFF at 3.0 minutes. The RTE integrator allows you to integrate the chromatograms using unique tools or filters such as "maximum number of peaks", and "area percent". The RTE is useful if you want to integrate the top "X" peaks based on area, such as the top 5 peaks by size. The Chemstation integrator is useful when you need timed events, such as when you have a varying baseline from something like column bleed in GC. The user has control over which integrator to use by using the menu items in the Data Analysis view.

16. I want to be able to get normalized data rather than having the ordinate on my mass spectrum being labeled as a function of the signal strength of the base peak. How can I do this? (id=128)

In the Command Line of the MSD ChemStation Data Analysis software (which is either just below the button bar below the Main Menu or at the bottom of the display below the normal position for the spectrum Window) type normalize, 100 and click on the Execute button or press the key. This will normalize the currently displayed spectrum (the spectrum in the X register) to be normalized to the most intense peak in the mass spectrum. It will also cause the spectrum Window (Window 1) to close. Now type draw, 1, X,,0:110 in the Command Line and click on the Execute button or press the key. This causes the normalized spectrum to be displayed in the Window at the bottom of the normal data analysis view. You can then view the data in a tabular format by selecting Tabulate from the Spectrum menu. If you want this display often, you may want to write a macro containing these commands. If you are using a version of G1701DA Data Analysis that supports the CustomTools buttons, you may want to put these commands into one of your CustomTools macros.