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Knowledge Base Results
Category: MSD ChemStation
Records returned: 83
MSD ChemStation
1. We have purchased a copy of the MSD ChemStation (G1701DA) software for use by the laboratory supervisor. She wants to be able to look at data and write data acquisition methods that can then be copied onto our computers used for data acquisition. This means that we have to get to the Method editors through Top. We cannot figure out how to make this work. (id=129)
When you run Configure on the computer without an instrument connected, the first dialog box displayed after selecting an instrument number to be configured (Configure Instrument) has a check box, Offline Instrument. Make sure this check box is selected.
The next dialog box (Mass Spectrometer) has a check box (Include a Mass Spectrometer in this instrument Configuration). Check this box and then click on the button labeled New MS Device. This causes the New Mass Spectrometer Device dialog box to be displayed on top of the Include a Mass Spectrometer in this instrument Configuration dialog box. The default Model is 5973N, 5973 inert MS. Accept this by ignoring this entry.
You will need to enter an IP Address The IP address has four positions separated by periods (.). Enter the numbers 10.1.1.101. Click on the OK button. This causes the New Mass Spectrometer Device dialog box to close. Highlight the entry you just made in the Mass Spectrometer Device Selection window of the Include a Mass Spectrometer in this instrument Configuration dialog box and click the Next button.
This causes the Mass Spectrometer Options dialog box to be displayed. Click the Next button. This causes the Set DC Polarity dialog box to be displayed. Accept the default of positive polarity by clicking on the Next button. This results in the Gas Chromatograph dialog box being displayed.
Follow the same instructions that are given above for the Mass Spectrometer using the IP address 10.1.1.102. Clicking the Next button in the Gas Chromatograph dialog box will result in the Data Analysis dialog box opening.
Select the desired Data Analysis type and click on the Next button. This causes the Review Configuration dialog box to be displayed which has all the settings you have entered. Clicking on the Finished button will result in the configuration you have set. When you now click on the Top icon for this instrument (usually Instrument #1), you will be able to access all the METHOD editors.
MSD ChemStation / Data Analysis
2. 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.
3. 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.
4. 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"Four lines down is:
Menucmd "Select C&hromatogram Labels...","enh_chromlabels","Allows selection of Peak Labels"Below this line insert the following four lines:
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
Save the file.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:.5Contents of Tile2.MAC
name tile2 Window 2,0:1,.5:1 Window 1,0:1,0:.5The display of the spectrum in the Y register is not automatic. In order to refresh the display of the spectrum in the Y register (spectrum on right side), it is necessary to select the Tile Two Spectra option from the Chromatogram menu. In order to have a single spectrum cover the bottom of the display, it will be necessary to select Tile One Spectrum from the Chromatogram Menu.
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.
5. 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.
6. 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.
7. 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 = ""TO: FONTAXIS = "gevena, 6,0,0" Save the changed file. Open ChemStation Data Analysis and you will have the correct font to read the labels on the vertical axis. This works when you are using the Enhanced Quantitation mode of Data Analysis.
8. 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.
- Open the File
- Select the File Menu
- Select the Select Signals option. If there are no separate signal files, this option is grayed.
- 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.
- Deselect the items you do not want to display when the file is opened.
- Click on the OK button
- 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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
MSD ChemStation / MSD Software Upgrades
18. I am looking to upgrade an old WIN 3.1 data system on a 486 computer for my even older Hewlett Packard 5970 MS/ 5890 GC system. The last time I checked with HP/Agilent (a few years ago) they claimed that the only way to upgrade the computer hardware to a Pentium machine required use of a network-based solution (If this sounds sketchy, please bear in mind that I am recounting a conversation which is at least a few years old, and was at the time only marginally understood)which cost about 16K! This seemed like a lot for a cheap computer and 500$ worth of software. Does anybody know of any vendors who have found lest pricey ways around this problem? Thanks (id=9)
There are companies that do suggest they can update your 5970 MSD. However, this is tricky proposition and some cases could be a problem. The simplest solution might be the "remote data analysis" alternative. I'm not sure about the 16K, but Agilent did provide a bundled solution that includes the data analysis software, PC and a contributed utility macro (copydata.mac). This macro is available from our website. The solution allows the remote data analysis computer to accept data files from the existing ChemStation and automatically process the files. At one time there was an application brief which described the setup. There may still be one issue. The existing ChemStation does need a networking interface card. As these ChemStations where all HP PCs, you need to follow up and find a card that will work. If you need some assistance in setting up your solution, please ," Ask Dr. ChemUser".
19. How do I upgrade from an \hpchem system to an \msdchem system? (id=135)
The Agilent MSD ChemStation installation software look to see if there is an existing version of the ChemStation on the computer. If there is an existing version, the installation program will attempt to install the new version on top of the existing version as a default. This means that if your existing version of ChemStation is installed in \hpchem and you accept all the defaults during installation, your new version of ChemStation will also be in the \hpchem folder.
This can cause a problem for the installation of other software from Agilent such as the NIST05 version of the NIST/EPA/NIH Mass Spectral Database. The NIST05 installation looks for ChemStation to be installed in the \msdchem folder. If the installation does not find this folder, it will issue an error dialog box on installation and abort the installation.
You can specify that the installation of the new version of the ChemStation software be in the \msdchem folder. However, this means that you will now have two versions of ChemStation on your computer. You are better off to uninstall the exiting version and then install the new version that will create the \msdchem folder.
First you will need to make a backup of all of your data, methods, and any custom macros that you may have written. The data are normally stored in a folder \DATA which is under the folders for the up to four instruments that may have been specified. The folders for each of these instruments have the names 1, 2, 3, and 4 and will be found in the \hpchem folder. The methods will be in a folder inside these instrument folders with the name METHOD. Your custom macros will either be in the folder \msexe or \msmacros, both of which are in the \hpchem folder.
Use the Start/Settings/Control Panel/Add/Remove Programs selection to uninstall the existing version of ChemStation. This will not remove the \hpchem folder. After making sure everything you want from the \hpchem folder has been saved, delete the \hpchem folder using Windows Explorer
You can now install the new version of ChemStation. As the installation runs, make sure that the software installs to the \msdchem folder. After the installation is complete and you have configured your instrument, you can restore the data, methods and macros that you backed-up from the previous installation. There is no assurance that all of your macros will still function; therefore, you should text them before using your new system.
MSD ChemStation / MS Libraries/ Databases
20. In the GC/MS MSD ChemStation I will set the NIST or Wiley library as the default library using the Spectrum/Select Library command. The next day when I start to use the ChemStation software, the default library is set back to DEMO.L. Can you tell me how to set the default library so it will not change? (id=5)
When the GC/MS MSD ChemStation Data Analysis opens it opens a DA Method. The Method is the default method, DEFAULT.M. This method contains the name of the default library to be used with the PBM search algorithm which is part of the ChemStation software. When you change the default library from DEMO.L to NIST98.L or WILEY7n.L, you make the change for the current session of DA. When you exit DA and restart the Program, the DEFAULT.M method is loaded and sets the default library to DEMO.L.
In order to have the default method set either the NIST98.L or WILEY7n.L as the default, you have to save the default method after selecting a default library. After using the Spectrum/Select Library command to select the desired libraries to be searched each time the ChemStation Data Analysis is used, select Method/Save Method. The Save Method As dialog box will appear. The name DEFAULT.M will be highlighted. The dialog box will also show the path of where this method is being stored. Place the Mouse pointer over the OK button and click the left Mouse button once. This will save the default method with the libraries you have selected. Now, each time you start the ChemStation DA you will have the desired libraries used.
Remember, there are limitations associated with the ChemStation PBM search. You are better off using the NIST Mass Spectral Search Program. This can be accessed from the Spectrum menu after you have installed the NIST ChemStation Macros. You can also set the ChemStation to use the NIST MS Search Program when you double-click the Right Mouse button with the Mouse pointer on a displayed bar graph spectrum.
To use the NIST Structures, you must select the appropriate *.sdb file. See the follwing FAQ for instructions on how to do this.
21. I purchased the NIST Structures with my Wiley 7n mass spectral database from Agilent. I installed this software as instructed. However, whenever I do a search by double clicking the right mouse on the spectrum, I get a search result but no structure. Can you help me? (id=6)
You need to set the structure library. Once you do this you do not need to save it as you do spectral libraries. Select View from the Main Menu in ChemStation Data Analysis. Select Parametric Retrieval from the View menu. This will cause the display to change from the Standard Menu mode to the Parametric Retrieval mode. The Search Parameters dialog will be displayed inside the Parametric Retrieval view. Put the Mouse pointer on the Cancel button and click the left Mouse button. This will close the dialog box.
Select Structures from the Main Menu Bar. Select Select Structure Database from the Structures menu. This will result in the Chemical Structures Databases dialog box being displayed. Place the Mouse pointer on the Add New File button and click the left Mouse button. This will cause the Chemical Structure Database Select file selection dialog box being displayed. This dialog box should display the contents of the \Database folder (directory). Many of the displayed folders will have a .L extension. These are the various databases that contain mass spectra. Look for either files with the extension .STB or folders that may contain these files such as \MOLSTRUC (NIST92 (NBS75K.L) structure are in MOLSTRUC.sdb. The NIST 98 structures database hase the name Struct98.STB and the NIST02 structures have the name subset,sdb and is in the \NIST02 folder. Highlight that file name by placing the Mouse pointer over the name and cliking the left Mouse button. Then place the Mouse pointer on the Open button in the lower right corner of the dialog box and click the left Mouse button. This causes the file selection dialog box to close and the Chemical Structure Databases dialog will become visible. The file name Struct98.STB will now appear in this dialog box. If the demo.STB is listised, you may want to remove it. Place the Mouse pointer on demo.stb in the dialog box and click the left Mouse button. This highlight the entry and un-grays the Move to Top and Remove from List buttons. Place the Mouse pointer on the Remove from List button and click the left Mouse button. The entry will be removed from the dialog box. Place the Mouse pointer on the OK button and click the left Mouse pointer. This removes the dialog box and the Struct98.STB structures database will become the default.
To return to the main DA display select View from the Main Menu Bar and then select Standard Menu from the View menu.
There is a PDF Instruction from Agilent on configuring strctural databases which can be downloaded at:
22. I've heard that the GC/MS MSD ChemStation allows the user to include chemical structures with mass spectra. Where can I get more information on how to do this? (id=12)
Yes.? Most recent versions of the GC/MS MSD ChemStation software allow the use of molecular structures within the software. Version G1034C and later support a structure database from Agilent, as well as the ability to import a custom structure in a .MOL format. The software does not support the actual drawing of the molecular structure. For this, you need a third party application. The specific steps for this are not well documented. For more information please send a request to," Ask Dr. ChemUser".
23. I am using the GC/MS MSD ChemSation. I have three selected libraries, the Wiley7N, NIST98, and one that I created on my mass spectrometer. These libraries are listed in this order in the Library Search Parameters dialog box displayed by selecting Select Library from the Spectrum menu in the Enhanced Quantitation mode of Data Analysis. Every time I do a search I only get hits from the Wiley 7N. Sometimes the match numbers are very low. This is true even when I search a spectrum that I have added to my library. What is happening? (id=51)
There is a box next to the first two entries in the Library Search Parameters dialog box labeled "Search Next Library if Match <". The default value is 0. This tells the program to search the next library only if the search of the first library results in no hits. This is usually never the case. You can enter numbers in these boxes from 0 to 99. If you enter a high value after the first library, any hits with a lesser match value will not be reported. Most users enter their own library first follow by the commercial data bases. One problem wth this type of search strategy is that hits with high match factors can be ignored. If the value for the user library is set at 85 and that for the NIST98 is set at 0, when only these two libraries are used, a hit of 83 from the user library will be ignored and not reported while, the best hit will be reported as 41 from the NIST98.
If you have purchased a library bundle from Agilent that has the NIST Mass Spectral Search Program and are using the Enhanced Data Analysis, when you installed the NIST MS Search Program, you installed a series of macros. One of these marcos (LS.mac) will search the three libraries in the Library Search Parameters dialog box and report the 20 highest match factor hits regardless of what library there were in. Select Spectrum from the Data Analysis menu bar. Select Multiple Lib PBM Search. You can use this macro with other forms of Data Analysis. You will need to read the documentation that comes with the macros. This can be found in the NIST MS Search Program?s program group.
24. When I create a user library I sometimes make a mistake in typing the name or at a later time I will find a better spectrum. I want to be able to edit this entry in my library. Both the GC/MS MSD ChemStation utility for dealing with user libraries and that used with the NIST MS Search Program will not allow me to do this. I don?t understand this limitation and want to know if there is any way to get around it. (id=52)
Each entry into a user mass spectral library (database) has a unique descriptor which is its record number. In order to defend the results of a search against a library, this descriptor must remain unchanged. If you could edit a record in a database, a search run before the edit would yield the results of one spectrum, while that run after the edit could yield the of another spectrum. Therefore, each edit results in a new record number with the old record being made inaccessible. You can have all the accessible spectra in a NIST MS Search Program library retrieved using the ID number search. These spectra can then be put in the Spec List and a new library created with consecutive record numbers.
25. What is the difference between the Library Search routine in the GC/MS MSD ChemStation and the NIST Mass Spectral Library Search when using the either the NIST or Wiley mass spectral databases? (id=81)
The GC/MS MSD ChemStation Library Search uses the probability based matching (PBM) algorithm developed by Fred McLafferty and colleagues. This is why you often hear this search referred to as a "PBM Search" to distinguish it from an NIST Search. The NIST MS Search uses a dot-product algorithm which was first introduced in the INCOS library search routine made popular by Finnigan Corp. The PBM search will often not retrieve the spectrum of the same compound as the analyte if the base peak of the two spectra are not the same. This is not the case with NIST Search. The PBM search is done on condensed spectra even though the full spectrum is used to display the hit (library spectrum match). You can remove the Full.d file from the NIST or Wiley database folders in the \Database folder and get the same results as if the file was still there. The hit display will be the only difference. The NIST Search is performed against the full spectrum.
26. Is the Wiley database better than the NIST database? The Wiley is a lot bigger. (id=82)
The Wiley database has a lot more spectra and a few more compounds than does the NIST/EPA/NIH Mass Spectral Database. In some cases it is best to have both. The latest revision of the NIST DB (NIST02) has 174,948 spectra of 147,198 compounds. When you look at spectra from the Wiley database in either the ChemStation library utilities or the NIST MS Search Program, you only see structures of compounds that have Chemical Abstract Services registry numbers (CASrn). The NIST DB has structures for all but two of its compounds even though it has only 107,105 unique CAS numbers. The NIST DB has no more than 3 replicate spectra, in addition to the main spectrum, for any of its compounds. The NIST DB has no duplicate spectra (the same spectrum entered more than once). This is not the case with the Wiley. Sometimes the same spectrum will be in two different collections and the Wiley database enters entire collections without any evaluation. The NIST DB has very few monoisotopic spectra. In addition to a large number of monoisotopic spectra, the Wiley database has a number of single-peak spectra. The last two versions of the NIST DB (NIST98 and NIST02) involved a great deal of spectral evaluation. This is why some compounds that had been listed in previous versions of the NIST DB can no longer be found in the current release. The spectra were incorrect. A good example is the spectrum for the unique elemental composition C4H6MnN2S4 ( M W 265). There are two spectra for this compound in the Wiley database. There was a spectrum for this compound in NIST92 but no spectra in NIST98 or NIST02. One of the Wiley spectra and the NIST92 spectrum for this compound are clearly the spectra of sulfur (S8). If your unknown spectrum was that of sulfur and you searched that spectrum against the Wiley database, you well could get a hit for the agricultural fungicide maneb. The NIST DB is a collection of better quality spectra than the Wiley database.
27. I am not sure I understand the difference between the Wiley7 and the Wiley7N. The Wiley7N is supposed to be the Wiley and NIST libraries combined. If I have the Wiley7N why should I buy the NIST? (id=83)
Both Wiley and NIST own some number of spectra jointly. All of these spectra are included in the Wiley database. However, some of these spectra have been replaced by better quality spectra in the NIST/EPA/NIH Mass Spectral Database. Some of these jointly owned spectra have been removed the NIST DB because they were found to be incorrect. As of the release of the NIST02 DB, the Wiley7N still only has spectra from NIST98. Therefore, one reason for getting the NIST02 would be because all the spectra currently in the NIST02 are not in the Wiley7N. Some compounds from earlier versions the NIST DB have been removed because the spectra were found to be incorrect. These spectra may well still be in the Wile7N because it is Wiley?s practice to not remove spectra. Generally speaking, the NIST DB is a collection of better quality spectra than the Wiley7N with fewer monoisotopic and single-peak spectra. In some cases, because of the spectra of additional compounds not found in the NIST DB, it is best to have both. The Wiley 7N is usually more expensive than the Wiley7. If you are going to get both databases, get the Wiley7 and the NIST, not the Wiley7N and the NIST.
28. Why do the spectra displayed from the GC/MS MSD ChemStation Pfleger/ Maurer/Weber library of Drugs, Pollutants, Pesticides and Metabolites look so different from the spectra in the NIST or Wiley libraries? Why won?t the NIST2LIB utility convert the PMW library to a NIST library? (id=84)
The answer to both of these questions is the same. The PMW database is distribute only in the condensed form (max 12 peaks for the ChemStation version). PMW require that a copy of there four volume set of books be sold with each electronic copy of the database. The NIST LIB2NIST only works with the Full.d file of a GC/MS MSD ChemStation Library. This file is absent, ergo, you cannot do a conversion. If you can get the PMW database in the NIST format from Finnigan, you will have more peaks per spectrum; however, there will be no more than 50 peaks per spectrum. If you get the PMW database from Varian in the INCOS format, you can use the Palisade Mass Transit program to convert it to the ChemStation format. This can then be converted with LIB2NIST. However, many of the spectra in this version of the PMW database are from an internal ionization ion tap mass spectrometer. This is why there are more spectra in this version of the databse than other versions. Before you change any library to another format, copy a libray, or covert a library, check the software license to mke sure that the distributor and/or publisher will allow this activity.
29. I have some old data that I have archived to a CD ROM. When I look at these data using the GC/MS MSD ChemStation and try to do a library search using the NIST Mass Spectral Search Program nothing happens when I double-click the right Mouse button on the displayed spectrum. A bell sounds and "File 55 is not open" appears in the bottom status line of the display. (id=88)
The marco that is used to pass a spectrum from the GC/MS MSD ChemStation Data Analysis to the NIST MS Search Program writes a text file in the folder that is the ChemStation data file. Because your data is on a CD ROM, it is not possible to write/create this file on this Read Only device. Copy the data file folder to your hard drive and do the data analysis from this device. The same problem exist when you have archived data to a network drive for which you do not have write-privileges. Updated Answer (20-Sept.-2004) You can download a new set of macros form the NIST MS Search Upgrade sit (http://chemdata.nist.gov/mass-spc/Srch_v1.7/CSsupport.html and click on the ChemStation Macros for V.2 button at the bottom of the page) that will allow you work with data files on a Read Only device. Copy these downloaded macro files over the macros that are in the \msexe folder. After you have installed the new macros, you MUST select Set Default Search Engine on the Spectrumm menu and chose Set NIST MS as Default Search to completely resolve the problem.
30. What MS spectral libraries/ databases are available for the GC/MS MSD ChemStation? (id=91)
The GC/MS MSD ChemStation libraries consist of 2 basic types: general and application specific. Although the MSD ChemStation has been around for some time, the basic libraries choices have remained pretty much the same. What has changed is the revision or compounds and spectra that are included. Currently the libraries available include: NIST98, Wiley7th N, RTL (retention time locking) Pesticides, Stan Pesticides, and Pfleger, Mauler, Weber (PMW)3rd edition drugs and metabolites. There is also a NIST chemical structures database. The structures DB will allow the return of a structure for any library spectrum that has a CAS registry number. The MSD ChemStation software also provides the functionality to create your own spectral and chemical structure databases.
31. What are the differences between the current GC/MS mass spectral libraries? (id=92)
Library #of spectra #of compounds Product Number NIST98 129,136 107,886 G1033A Wiley7th N 390,000 316,934 G1035B Stan Pesticides 340 340 G1038A PMW(1) 3rd 6,300 6,300 G1039C (only condensed spectra) RTL Pesticides 567 567 G1049A NIST Structures NA 108,173 G1036A (1) Pfleger, Maurer, Weber drug and metabolites.
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32. I downloaded a copy of the NIST MS Search Program v.2.0 from the NIST Web site (http://chemdata.nist.gov). I installed it in my NIST directory. The program works fine. However, when I called it from the MSD ChemStation, I got v.1.7a. I removed all vestiges of v.17a and then I got a DOS Run error. What’s going on. (id=110)
When you downloaded the v.2.0 of the NIST MS Search Program, you should have also downloaded new versions of NIST/ChemStation macros that are specific to v.2.0. The v.17a macros look in WIN.INI for the path of v.1.7a and these macros call NIST$.EXE. The v.2.0 macros look for the path for v.2.0 of the NIST Program and call NISTMS$.EXE. You can sometimes get by by changing the NISTMS$.EXE name to NIST$.EXE, but you are better off downloading the correct version of the macros. You do not need to change any of ChemStation menus, just replace the NIST macros in the \MSEXE directory. Complete instructions are found on the NIST Web site.
33. Whenever I try use the NIST MS Search Program, I get a File 55 Not Open error in the message bar at the bottom of the ChemStation display. (id=111)
There are two primary reasons for this. The first has to do with the data files being on a READ ONLY device like a network drive or a CD ROM. The second is that you made a copy of a data file (actually, a directory) that you had previously done an NIST MS Search search on to a CD ROM and restored it to your hard drive. Whenever you copy files to a CD ROM they are flagged READ ONLY and remain that way until you change their status, even if you copy them to a non-read only device.
The macros that allow for interactively between the ChemStation and the NIST MS Search Program write a file that contains the spectrum to be searched in the directory that is the data file. This file will have the name of the data file (without the .d extension) and a .msp extension. If the data file is on a READ ONLY device, the file cannot be written. If the data file folder contains the msp file and that file has been flagged READ ONLY, the file cannot be over written. Look at what your situation is and make the appropriate alterations to your system. Copy data files from READ ONLY devices to a directory where the MSP file can be read or change the properties of existing MSP files from READ ONLY.
34. I just upgraded from NIST MS Search 1.6d and the NIST98 Database and now I cannot get the spectra into the NIST Search Program. I can?t find anyone to help me. (id=113)
You probably upgraded to version 2.0 of the NIST MS Search Program using Agilent P/N G1030-60967 and are using a version of the ChemStation earlier than G1701 DA Version C With this version (and higher) of ChemStation, support for the WIN.INI file was discontinued. Now all information as to ChemStation file locations is stored only in the Windows Registry. A version of the Macros used to put spectra in the NIST MS Search Program was thought to have been designed to get the location of the ChemStation software from either the Windows Registry or the WIN.INI file. However, the single Macro word that was supposed to do this only cause the retrieval from the Windows Registry. As a user of an earlier version of ChemStation, the location of the software is not recorded in the Windows Registry, it is recorded in the WIN.INI file. This errant Macro will write the primary locator file HPNIST.TXT in your system root directory; i.e., C:\. The AUTOIMP.MSD file in your NIST MS Search Programs directory will have the NIST Program look in the \HPCHEM or \MSDCHEM directory for this primary locator file.
You have two choices. The first is to edit the AUTOIMP.MSD file. This is a text file with a single string. Open it using Notepad. Edit the contents so that they read C:\HPNIST.TXT. If you are using Windows 95 or Windows 98, be careful that Notepad does not extend *.TXT on the end of the file name; e.g., AUTOINP.MSD.TXT.
The second choice is to download an updated version of the NIST MACROS. Go to
35. I upgraded my GC/MS ChemStation software to G1701DA ver D.00.00.38. I then reinstalled my Mass Spectral Libraries NIST 98 Rev. D.02.00. Before, when I installed this version of the NIST Database, I had several options on my Spectrum menu (e.g., PBM Quick Search, NIST Search, Multiple Lib PBM Search, Set Default Search Engine, NIST Output, and AMDIS). These options no longer appear on my Spectrum Menu. What can I do to get them back? (id=114)
When Agilent came out with G1701DA, they decided to modify all the macros that are responsible for the data analysis Menu Bar to work with the NIST MS Search Program, if it is installed. NIST created the file necessary for this to work. This is the nistmenu.mac file. This file is not on your NIST installation disk. Download the NIST v.1.7 macros from
36. We have the GC/MS MSD ChemStation with the NIST Mass Spectral Search Program. When we teach classes, we do not want our students to use the library to identify their unknowns. Do you have any suggestions as to how to disable the library search. (id=120)
You did not say which version of the NIST MS Search Program you are using or whether or not you have the NIST/EPA/NIH MS Database in the Agilent format (NIST98.L). This answer addresses all of these scenarios. The simplest way to disable the NIST MS Search Program when used as the default library search option of the ChemStation is to turn automations to the off position. In v.2.0 of the MS Search Program, select the Library Search Options button (4th button from the left next to the drop-down box at the top of the Lib Search tab?s display) Deselect the "Automation" check box in the Other Options portion of the Search Tab of this dialog box. Then point to the OK button with the Mouse pointer and click the left Mouse button. When you put the Mouse pointer on a displayed spectrum in ChemStation and double-click the Right Mouse button, the NIST MS Search Program will be brought into focus and the spectrum will be added to the Spec List pane of the Lib Search tab; but, the search will not be carried out. In versions of the MS Search Program prior to v.2.0, select Search from the Main Menu bar. Put the Mouse pointer on the Automation button on the right side of the User Search Options dialog box and click the left Mouse button. This will result in the Automation dialog box being opened. Deselect the "Automatic Search On" check box. Point to the OK button and click the left Mouse button to close the Automation dialog box. Point to the OK button and click the left Mouse button to close the User Search Options dialog box. This will result in the same behavior as described above for v.2.0 when the library search is requested from the ChemStation display. REMEMBER: After you no longer wish the library search to not function, you MUST turn the "Automatic Search" ON. If you are using the Agilent PBM search as your default library search, with the NIST02.L Database, another version of the NIST/EPA/NIH Database, or some other database, you can cause this database not to be searched by changing the default library to the DEMO.L library. From the ChemStation?s Main Menu bar, select Spectrum. From the Spectrum menu, select Select Library. This will result in the Library Search Parameters dialog box being opened. The top entry line will contain something like "c:\Database\NIST98.L" (NBS75K.L is the 1992 version of the NIST/EPA/NIH Mass Spectral Database, NIST98.L is the 1998 version, NIST02.L is the 2002 version; and Wiley6.L and Wiley7n.L are versions of the Wiley mass spectral database). Assuming default conditions, you will select the DEMO.L library from the \Database directory. The way this is accomplished varies depending on the version of the ChemStation you are using. For versions prior to G1701 DA D.01.00, highlight the top entry and type ?. This will cause Browse For Folder dialog box to open. Point to the DEMO.L folder and click the left Mouse button to highlight it, and then point to the OK button and click the left Mouse button. This will cause the Browse For Folder dialog box to close and the top entry in the Library Search Parameters dialog will be "C:\Database\DEMO.L". If there are any databases in the two following entry spaces, these should be deleted. Point to the OK button and click the left Mouse button. Now, when a spectrum is pointed to and the Right Mouse button is double clicked, the DEMO.L library, which has only 10 spectra, will be searched. If you do not want to effect the previous settings, Select Method from the Main Menu bar. Select Save Method from the Method menu. This will cause the Save Method As dialog box to be opened. Type a name of no more than eight characters in the Method File: text entry box; i.e., Student. Point to the OK button and click the left Mouse button. This will become the default method for the ChemStation?s data files acquired by students. CAUTION: If a previous acquired data file is opened, and its Data Analysis Method is also opened, then that newly opened Data Analysis Method becomes the default, which may reactivate the full-featured library search of a major DB. REMEMBER: A Data Analysis Method remains the default until it is changed. In order to restore the full-featured PBM library search, you must restore the original Method.
37. Our Library Search has stopped working. When I double click on the spectrum in the GC/MS ChemStation with the Right Mouse button, the library search display appears but the results are always the same and it does not appear that the search was carried out. What?s wrong? (id=121)
You did not say whether you were using the NIST MS Search Program or the Agilent PBM search routine. Assuming you are using the NIST MS Search Program, the results listed in the Hit List are those from a previous search. If your spectrum has been added to the Spec List (the top name in the Spec List will have the Name of the Agilent ChemStation data file and the spectrum?s number and time), then you should check to see if Automation has been turned off. In v.2.0 of the NIST MS Search Program, the automation settings are in the Library Search Options dialog box?s Search tab (selected by clicking on the Library Search Options button; 4th button from the left next to the drop-down box at the top of the Lib Search tab?s display). In previous versions, this setting is in the User Search Options dialog box accessed by selecting Search from the Main Menu bar. If the NIST MS Search Program is brought into focus and the spectrum is NOT added to the Spec List, there may be a problem with the contents of the AUTOIMP.MSD file that is located in the same directory as the NIST MS Search Program (C:\NIST02\MSSEARCH\ by default for v.2.0). The contents of this file should be c:\MSDChem\HPNIST.TXT" or c:\HPChem\HPNIST.TXT, depending on the drive used for the ChemStation software and the directory created at the time of the first installation of the ChemStation. If the contents of the AUTOIMP.MSD files are correct, check to see if you can determine the location of the temporary file HPCHEM.TXT. If this temporary file is located in some directory other than that identified in the AUTOIMP.MSD file, change the AUTOIMP.MSD file to reflect this location. If your problem is associated with the use of the Agilent PBM search, make sure that the NIST/EPA/NIH Mass Spectral Database or one of the other PBM search databases supplied by Agilent is the default library. See FAQs 17 and 18 for additional information on how to check and install libraries and structure files used with the PBM search. check and install libraries and structure files used with the PBM search.
38. I have GC/MS MSD ChemStation mass spectral libraries that I want to convert for use in the NIST MS Search Program; how do I do this? (id=122)
Select the Start Button on the Windows Desktop. Select Programs. Look for the NIST Mass Spectral Database folder and select it. Select the program Lib2NIST Converter and Follow the prompts. If you have a structures library that is associated with the GC/MS MSD ChemStation mass spectral database, make sure the *.IND and *.SBD files for that structures DB are in the *.L folder that defines the MSD ChemStation mass spectral database. These structures will then be associated with the created NIST MS Database.
39. I have some NIST MS Search Program user libraries and I want to convert them to libraries in the GC/MS MSD ChemStation format; how do I do this? (id=123)
Export the Spec List from the NIST Program as an MSP File (Librarian tab). Use the Lib2NIST conversion Program on the NIST Selection from the Start/Programs menu. Convert the MSP file to an HP JACP (HPJ) file. Start the ChemStation Data Analysis. Select View/Parametric Retrieval from the Main Menu Bar. Click the Cancel button on the dialog box that opens. From this new screen's Main Menu Bar, select Library. From the Library menu, select Read JCAMP File. Select the file that was created with Lib2NIST. Click on the Open button. The File Select dialog box will close and a new dialog box will open asking you to enter an Agilent Library name. Enter the name of the new library. When you click on the OK button, a *.L with the entered name will appear in the \database directory.
40. I am using the NIST MS Search Program v.1.6d. Sometimes when I send a spectrum from my Agilent Data Analysis program, I get the error message "File is not a library, or file is too large". (id=126)
Check the file with an MSP extension created by the Agilent software. This is a text file and can be opened in Microsoft Notepad. You will find that it has more than 800 m/z ? intensity pairs. Versions of the NIST MS Search Program after v.1.6d do not display this error message, but they create spectra in the NIST MS Search Program with a maximum of 800 pairs. You can upgrade at http://chemdata.nist.gov.
41. We just upgraded to G1701 D.01.02 of the MSD ChemStation and now our NIST MS Search Program does not work sometimes when we double click the Right Mouse button with the Mouse Pointer on the spectrum display. We get an error dialog box with the message:
Error: file is not a library, or library is too large.
The next line has:
C:\MSDChem\1\ProjectData\XRV_091804STDData\STDMix_092_25uL.d\STD_Mix_092_25uL.msp
We downloaded NIST MS Search v.2.0b, but we still cannot get the spectrum to import to the Spec List. (id=131)
A. As of G1701D 0.01.00, it was possible to create data file names with up to fifty characters in the MSD ChemStation. This is the so called "long-file-name" application. There was a bug in the NIST MS Search Program v.2.0a, which is the version distributed by Agilent Technologies, that prevents the importing of spectra with file names and paths having more than a specific number of characters. This NIST MS Search bug in v.2.0a is what causes the display of the Error dialog box you have described. NIST MS Search v.2.0b did not fix the problem; however, it prevented the Error dialog box from being displayed. In v.2.0b, the NIST MS Search is brought into focus by the ChemStation macro, but the spectrum is not prepended to the Spec List. A new set of macros, that can be downloaded form the NIST MS Search Upgrade site (http://chemdata.nist.gov/mass-spc/Srch_v1.7/CSsupport.html and click on the ChemStation Macros for V.2 button at the bottom of the page) will resolve the problem. Copy these downloaded macro files over the macros that are in the \msexe folder. After you have installed the new macros, you MUST select Set Default Search Engine on the Spectrumm menu and chose Set NIST MS as Default Search to completely resolve the problem. These macros were original modified to addresses a problem with using data files on Read Only devices. These modifications, serendipitously, also resolved the long-file-names problem.
42. We purchased an upgrade to our NIST Library from a company other than Agilent. They told us that it was in the ChemStation format. We ran the setup program for the NIST. When we try to select the new DB from the Select Library option on the Spectrum menu, we can?t find the NIST02.L file in the Database folder or in any other folder. (id=134)
Most third-party suppliers of the NIST/EPA/NIH Mass Spectral Database in the ChemStation format supply you with the NIST MS Search Program installation CD, which installs the DB in the NIST format. If you accept the defaults throughout the installation, this will also set the NIST MS Search Program as your default double-Right-Mouse-button-click search.
If you want to use the PBM Search with the NIST02 DB, you will have to copy the \NIST02.L folder from the supplied CD to the \DATABASE folder on the computer with the ChemStation. The \NIST02.L folder has the NIST\EPA\NIH Mass Spectral DB in the ChemStation format, and it also has the two files necessary to display structures with the PBM search results. When you configure your structure DB in the ChemStation, you need to select the subset.sdb file that is in the \NIST02.L folder.
The \NIST02.L folder is only automatically installed from the NIST02 Installation CDs purchased from Agilent Technologies. You have to copy this folder to your \DATABASE folder when you purchase from any third party.
43. We just installed an upgrade to NIST Library. Now we get some weird-Harold display that we have never seen before. (id=133)
When you installed your NIST/EPA/NIH Mass Spectral Database, you also installed the NIST MS Search Program. By accepting the defaults throughout the installation process, you have set the NIST MS Search Program as the default library search routine, replacing the PBM Search, which is part of the ChemStation software. You can cause the PBM Search Program to become the default if you want. The instruction to do this can be downloaded from the Agilent FAQ site at
44. I understand that a structure can be searched against the structures in the NIST Mass Spectral Database using the NIST MS Search Program to return spectra and compound information. How is this done? (id=136)
Draw a structure in any structural drawing program and then copy the structure to the Windows Clipboard. You can also copy structures in the associated with entries in the NIST Database or User Libraries from the from the NIST MS Search Program to the Windows Clipboard. This is done by displaying the spectrum that has the associated desired spectrum; point to the spectrum with the structure displayed, click the Right Mouse button; and select Copy Structure to Clipboard from the displayed menu.
After you have the structure to be searched on the Windows Clipboard, place the Mouse pointer in Spec List pane of the Lib Srch window (usually the upper left pane). Click the Right Mouse button. Select Insert Clipboard Structure from the displayed menu (This menu option is grayed if there is no structure in the MOL file format on the Windows Clipboard).. A structure dialog box will be displayed. The structure will be displayed. There are two field which can be populated: Name and Comment. The Name field will contain Clipboard # followed by a numeric symbol, by default. Put the Mouse pointer on the OK button and click the left Mouse button. The structure is inserted into the Spec List pane and is displayed in the pane just to the right of the Spec List. To search the structure, place the Mouse pointed on the structure Name in the Spec List; then place the Mouse pointer on the Structure Search button (to the right of the GO button) and click the left Mouse button. Structure search options can be set in the Library Options dialog box.
MSD ChemStation / RTL (Retention Time Locking)
45. My lab performs high volume analysis of relatively routine, yet complex samples. Often we experience retention drift that requires us to manually re-calibrate and process our data. Is there a way to adjust the retention times automatically? (id=17)
Revision B.01.00 or later GC/MS MSD ChemStations (G1701BA/G1710BA) include a feature that automatically monitors and updates retention time drift associated with routine column and pressure related drift. This feature requires a 5973MSD/ 6890GC (with electronic pressure control)and autosampler (ALS). “Closed Loop” Retention Time Locking is a feature in “Enhance” mode of data analysis. Check out GC/MS MSD ChemStations On-line Help, or for a more specific question, Ask Dr. ChemUser.
46. I have heard that the GC/MS MSD ChemStation has the ability to lock retention times and automatically update calibration retention times. What do I need to implement this functionality? (id=18)
?Closed Loop? Retention Time Locking (RTL) is a standard feature of the GC/MS MSD ChemStations (G1701CA/G1710CA) revision C.00.00 or later. It is implemented in the ?Enhanced? mode of data analysis.
47. I am currently Screening for pesticides using GC and GC/MS and heard there was a pesticide library for use with Retention Time Locking. How can I get access to this database? (id=19)
The G1049A RTL Pesticide Screening library contains 567 environmental pesticides/ chemicals and is sold separately. It requires GC/MS MSD ChemStations (G1701BA) revision B.01.00 or later. It also requires Electronic Pressure Control (EPC) for the Agilent GC.
48. I would like to use RTL (retention time locking) on just GC data. Is this possible? (id=20)
Yes. The G1701BA (B.01.00) GC/MS MSD ChemStations software supports RTL and instrument control and data acquisition for the 6890GC. No MSD is required. Infact, the software will conrtol up to 4 GCs. Need more details? Ask Dr. ChemUser.
49. How do I create my own “custom” Retention Time Locked screening library? (id=21)
There are three 3 basic steps for creating your own RTL screening library. The process requires appropriate experience with Library search and “Enhanced” mode of Data Analysis (G1701BA, B.01.00). The three steps are:
1)Create a GC/MS method that is RT Locked. 2)Create a MS library from samples analyzed with the RT Locked method. 3)Converting the library to a screening database.You will also need to know for each compound; the compound name and retention time in seconds. Additional information is optional. The actual steps involved are beyond the scope of the FAQ format. For more detailed information “Ask Dr. ChemUser”.
50. What are the advantages of Retention Time Locking? (id=22)
RTL is best used when:
1. moving a method to a different instrument system (like hardware components) 2. validating the system performance and for later comparison 3. after column maintenance (changed or trimmed) 4. general troubleshooting (pressure leaks) 5. to compensate to different detector outlet pressures
51. How does Retention Time Locking (RTL) screening software work? (id=23)
When used with the G1049A RTL Pesticide library, the GC/MS data is acquired using a method provided with the library (RTLPEST.M). The software then uses a narrow RT window to compare ions near the expected elution times in the library to those in the acquired data file. Retention times and ion abundance are used to determine possible hits. The result review functionality is based on the “Enhanced” mode Qedit feature and simplifies the interactive review/ confirmation process.
52. Are there any instrument configuration limitations when using Retention Time Locking (RTL)?K (id=24)
Yes. The RTL functionality is supported only on 5973A/N MSDs and 6890GCs with Electronic Pressure Control (EPC).
MSD ChemStation / Custom Reports
53. I currently use the MSD ChemStation and I have a need to create a special report specific to the needs of a client. What applications are compatible with the software? (id=28)
Data file formats (GC, LC and MS) can be exported in the Excel™ format via commands in the GC/MS MSD ChemStations . In addition, the GC/MS MSD ChemStations includes a “custom”-reporting reporting module that behaves much like Excel and has special commands that pull information directly from the GC/MS MSD ChemStations . The “Custom Reports” module allows you to create simple changes to a report, create completely new report formats and even perform trend analysis, all from within the GC/MS MSD ChemStations software.
For more info, try the GC/MS MSD ChemStations software On-line help or Ask Dr. ChemUser.
54. I would like to use the custom reports package of the MSD ChemStation to create a special report. What type of information is supported in the custom reporting software? (id=29)
Because the “Custom Reports” software is integrated into the MSD GC/MS MSD ChemStations , there are over 100 specific pieces of sample and result information that can be directly imported into a custom report format. The basic categories are: >Sample information, >Compound information, >Target RT information, and >Graphics information (spectra, chromatograms, etc.).
For more detailed information, see the GC/MS MSD ChemStations On-line Help or Ask Dr. ChemUser.
55. How does the GC/MS MSD ChemStations custom reports software work? (id=30)
The GC/MS MSD ChemStations sample and result information is extracted by pre-defined variables with in the GC/MS MSD ChemStations software and automatically imported into the Custom Reports module. These variables/ data types are selected via a “wizard” when creating a custom report “template”. Once the template is created, a method is associated with the template and when the method is processed, the appropriate method information is extracted from the GC/MS MSD ChemStations and imported into the template. The result is a report containing just the information selected via the “wizard”. Re-positioning and formatting of the information can further enhance both the template and custom report. Reports and templates may be saved and re-processed with out re-processing the method.
56. Can GC/MS MSD ChemStations custom reports be imported into other 3rd party applications? (id=31)
Yes, custom reports and information (including graphics) can be imported into third party applications such as Microsoft Office™. However there are some revision compatibility considerations. The best test is to try it. Most recent revisions of custom reports are Excel 95 file compatible. Current Microsoft™ office applications do read older files. Once a report is imported, it can easily be saved as the latest version.
57. I use the GC/MS MSD ChemStations for routine drug screening and would like an easy way to QA the internal standards. Will the GC/MS MSD ChemStations software allow me to do this or will I need a third party application? (id=32)
The GC/MS MSD ChemStations Custom Reports module does support the ability to do trend analysis and subsequently creation and implementation of control charting. By creating your own custom database, you can maintain and easily monitor trends as well as define control limits that are displayed on the chart (relative, percentage, and standard deviation). For more information, see the GC/MS MSD ChemStations On-line Help or Ask Dr. ChemUser.
58. I’m currently using the custom reports module from the GC/MS MSD ChemStations and would like to import files into Excel. Is this possible? (id=33)
Custom Reports and templates can be imported directly into Excel 97™ and Word 97™ in an Excel 95 format. Other applications compatible with Micrsoft Office(tm) products may also be possible. Try it or Ask Dr. ChemUser for assistance.
59. What GC/MS MSD ChemStations software revisions include the custom reporting tool? Is it possible to purchase custom reports separately? (id=34)
Custom Reports was first introduced with revision G1034 Software and later enhanced with a report creation "wizard" (G1701AA A.00.00) and then again with graphics functionality (G1701BA B.00.00/01. Custom Reports is not sold separately. However, a Data Analysis package G1710BA/CA/DA of the software is sold separately and for a modest price does include Custom Reports. If you have an older version of the GC/MS MSD ChemStations software, you may consider the purchasing of the stand-alone data analysis and off-load your processing and reporting. The Remote Data Analysis software software will allow you to transfer files from the older MSD system to a networked PC running the remote data analysis and "Report Manager" functionality. This operation can be manual or automatic. Up to 4 GC/MS MSD ChemStations systems can be networked. Additional information about remote data analysis can be found in this knowledge base, direct from Agilent Inc., or from our own Dr. ChemUser.
MSD ChemStation / Report Manager
60. What is report manager and why would you use it? (id=40)
One of the many unique features of the MSD ChemStation is a functionality called “Report Manager”. Report Manager is a method-processing engine that queus and executes defined methods for up to 4-networked MSD ChemStations. Once configured and started, it can automatically process data from all 4 ChemStations simultaneously. It typically is used in cases of high volume routine analysis or when unable to upgrade older systems to the newest software functionality.
As Report Manager is an advanced functionality of the MSD ChemStation, we suggest that you look for someone with past experience to speed your implementation or Ask Dr. ChemUser.
61. How much flexibility is there in using report manager for remote data processing? (id=41)
There are four basic ways to process data using Report Manager.
- Completely automatic: ?this includes data transfer and processing.
- Semi-automatic: auto file transfer and a manual start from within Report Manager
- Semi-manual: auto file transfer and manual processing via the DoList data analysis functionality.
- Manual: manual data file transfer and DoList processing command.
MSD ChemStation / Secured Control
62. Is it possible to protect my GC/MS system from inexperienced operators performing routine analysis? (id=108)
Yes, Starting with G1701AA MSD Chemstation software, a new feature was introduced called Secured Control (SC). SC is accessed from the MS TOP window. It allows the system responsible operator or manager to define multiple access levels for users based on user name and password.
Caution: As SC is by definition a security function to provide a secure environment; you should spend time to understand its functionality prior to implementation. We suggest you do the following: 1. Read all on-line help regarding SC and Report Manager. 2. Keep track of all user names and password information. Without it, you may need to reload the software. 3. Practice with the system when you have the appropriate time to understand its operation.
This is a great feature for any routine lab that may have inexperienced operators or multiple users.
MSD ChemStation / Remote Data Analysis
63. I have an older version MSD ChemStation system and would like to upgrade to the latest revision of software. As I understand, it can not easily be upgraded. My application is routine and my system works quite well. What are my choices? (id=35)
The ?Data Analysis? functionality found in the MSD ChemStation software is also sold as a separate installable application. The data analysis only product was first introduced as G1710AA circa 1996. All recent revisions also have a data analysis only product. The advantage of this product is the ability to load the software onto a second PC (your desk or bench) and use it to interactively or automatically re-process GC or MS data. When networked to your current MSD ChemStation system, the data analysis only software can now replace the older data analysis functionality and using ?Report Manager? functionality allows access to all the new features. Although there are some limitations, in most cases you will be able to process your current methods using the new software. The same G1710XX Data Analysis software is often bundled into a complete ChemStation system (G1717XX) including the PC and file transfer software (macro).
64. How does the MSD ChemStation remote data analysis data processing work? (id=37)
There are three basic steps:
> Set up a network connection between the two ChemStations.
> Data processing methods are loaded onto the remote ChemStation.
> A special macro [copydata.mac] is used to identify the location of incoming files and automatically imports them.
> Once imported, remote data analysis uses the method to process the data.
> Once configured and started, it can process data from up to 4 ChemStations.
65. What’s the best way to connect my two MSD ChemStations? (id=38)
Two PCs can either be connected in a peer-to-peer direct connection, via a Hub or direct to an existing LAN. If one or the other is connected to the company network, consult your IT department before setting up the connection. They may have specific protocols for this. With older MSD ChemStations you may have difficulting finding a networking card for the PC and configuring older versions of Microsoft Windows(tm) operating systems. As this is outside the scope of a simple Q and A, we suggest that you consult Agilent, your IT or if you need specific assitance, please Ask Dr. ChemUser.
66. Are there any limitations when connecting the instrument controller PC with the remote data analysis pc? (id=39)
There are a few things that you should be aware of. They fall into two categories: limitations of the remote data analysis processing system and file protocols.
Data analysis: This functionality only supports data processing. Any sequence related activity, such as auto or re-calibration must be performed manual using a post-processing step on the remote data analysis ChemStation. Performance may also be an issue. We suggest the remote pc have extra RAM and for reports, a printer capable of printing greater than 20 pages/minute. Keeping track of reports will also require some attention, as the reports are not collated. Even though the Data Analysis software supports multiple modes of data analysis, only one mode may be used (i.e., Enhanced)
File protocols: File names (all) must be no larger than 8 characters and share drives use the NetBEUI protocol.67. I?m attempting to set up a networked data analysis ChemStation for 3 Agilent systems: 1 GC/MSD and 2 GCs. I?ve heard this is possible. Do I need any special software to do this? (id=87)
The latest versions of data analysis software do allow this configuration. There are two software modules required to implement this. First, you will be using the ?Report Manager? functionality that already exists in the latest versions of MSD Data Analysis ChemStation software (G1710XX) or later). You should purchase the newest version if you do not already have it. Second, you will need a special macro for transferring files from the other three ChemStations. This special macro is called [copydata.mac] and is included in the G1717XX Data Analysis bundle. If you did not purchase the DA bundle, you may request the macro from Agilent Inc. The part number is G1717-60011. We suggest you request the Agilent application note 5968-2696E (may be discontinued) for an overview of how this process works. It is a little complicated and knowledge of Report Manager is helpful. If you need additional assistance please Ask Dr. ChemUser.
68. What versions of MSD ChemStation software support remote data analysis with a second ChemStation? (id=45)
We need to consider both the “Acquisition” ChemStation and the “Remote” ChemStation. The acquisition ChemStation acquires data from the instrument. The remote ChemStation will do the processing. Listed below are the compatible software revisions for both acquisition and remote ChemStation and instruments that are supported. The further back you go in software revisions, the more problematic the implementation becomes.
Acquisition ChemStations: G1034C (C.03.04); G1701AA (A.03.02); G1701BA (B.01.00); G1701CA (C.00.00)
Remote Data Analysis ChemStations: G1710BA (B.01.00); G1701CA (C.00.00) Instruments Supported: MS Engine; 5970/71/72/73 & 73N69. We have 3 GCs attached to one ChemStation (version A.09.01 (1R06) over Win NT 4.00.1381. We would like to run the system remotely via modem and alert the operator at home in case of a malfunction during the measurement process. We are planning to install a remote control PC software like Laplink but are not sure. Is there any macro or application software working with the GC ChemStation enabling remote control via a network or a modem thru a 2nd PC? (id=115)
Agilent has been using Carbon Copy32 and modem for remote support for many years. This seems to work very well. There are some considerations with regards to revisions and operating systems. We have also used it with good success. The remote access is quite straightforward to implement. However, if you have an older system (PC) you may have some difficulty finding a compatible networking interface. Regarding a system failure. In order to address the issue of system failures, we would need to know exactly what the failures where and the limits associated with each. It is possible in many cases to provide failure notification. For example send an email if a defined failure does occur. However, this is very specific to the application.
MSD ChemStation / Macro Language
Where do I begin if I want to learn how to write my own macro for the GC/MS Agilent ChemStation?
(id=43)Try to get hold of the Hewlett Packard manual, part number HP G1034-90034. It's a book called "Using and Writing Macros", but unfortunately it's out of print now. There's also a macro writing class offered by Agilent now, somewhere in the east coast, so check their class schedule. ChemUserWorld.com also teaches on-line classes on macro programming.
What macro command shows me the variables and macros that are currently loaded into the ChemStation's memory?
(id=67)The REM macro command shows you the variables and macros that are currently loaded into the ChemStation's memory. Be careful, it was designed to REMove them from memory, but you can use it to view them too.
What macro command shows me the commands and functions that are currently loaded into the ChemStation's memory?
(id=68)The macro command COM shows you the commands and functions that are currently loaded into the ChemStation's memory.
Is the ChemStation macro language case sensitive?
(id=69)No, the ChemStation macro language is not case sensitive, with rare exceptions, such as the DONTASK parameter for the "DELETE" macro command.
What type of debugging tools are there for the macro language?
(id=70)The best debugging tool is probably the "LOGGING" macro command. You can run it at the command line, or place it at a strategic location inside your macro. Typically, you first turn logging on to record everything that occurs to a text file. Then you turn logging off and examine the text log file for errors. An example is: LOGGING 1,"C:\temp\log.txt",1,1,1,1,1 folowed by LOGGING 0.
Another useful technique is to place "PRINT", "SLEEP", or "ALERT" commands at strategic points in your macro, especially if you have a hint where the error is occurring.
How can the ChemStation macro language communicate with other Windows programs?
(id=73)The ChemStation macro language communicates with other Windows programs by using a simple technique known as dynamic data exchange, or DDE. Several DDE macro commands are available. These DDE techniques were very useful before 32 bit programming became widely used, and they still work today.
What type of error handling techniques are there with the macro language?
(id=75)The "ON_ERROR" macro command is your best bet to use when handling errors. It will do almost whatever you code it to do when an error is encountered. For example, it can run another macro or run another macro command.
What are macros, how do I make them, and what are they used for?
(id=77)A macro is a list of ChemStation commands or instructions that are stored together in a text file that you most likely create with the Windows NotePad program. There are many ways to load this macro into the ChemStation memory environment so you can run or execute it. Macros are useful for automating tasks that you find yourself repeating over and over again that otherwise force you to use many mouse clicks, menu selections, and typed entries into dialog boxes. Macros are widely used to perform custom actions such as printing a unique report or interfacing with other Windows programs.
Are there any variables that the ChemStation creates that I can use in my macros?
(id=79)Yes, there any variables that the ChemStation creates that you can use in your macros. These are called system variables. Most of them begin with the underscore character, or "_", and are all capital letters, such as "_DATAFILE$." To see all the variables, use the "REM" command, but be careful because REM is used to temporarily REMove variables.
I am looking at the variable names in the ChemStation using the REM command and see that there are many that start with the underscore ("_") character. What is the significance of the underscore in their name?
(id=99)Variables that start with the underscore are referred to as system variables. They are created and modified by the ChemStation, and you can use them in your macros. In general, you can use them, but, they cannot be modified unless you use the VARLOCK macro command.
MSD ChemStation / Accessory Compatibility
80. What GCs and GC detectors are supported by the MSD ChemStation? (id=48)
This is based on revision. In general, with G1701AA revision A.00.00, control of the 6890 GC became possible and later the 5890 (A.01.00). It was not until later, that the software actually supported acquisition.
G1701AA rev. A.03.00 supported: FID, TCD and ECD
G1701BA rev. B.00.01 added: NPD, uECD, and single FPD
MSD ChemStation / Data Acquisition Methods
81. In MS SIM experiment on HP MSD, is it necessary to list the ions in an increasing order. If so, how about if I want to add a new ion that comes in between two ions. Should I delete and add, or should I be able to insert without deletion. (id=117)
You should be able to insert a new SIM ion without having to delete any existing ones. To add another ion to your SIM method: (1) Use the Edit Entire method from the TOP view under Method (2) Get to the MS SIM/Scan Parameter form (3) Set the Acq mode to SIM (4) Get to the MS SIM Parameters section (5) Enter your masses IN ANY ORDER in the M/Z box (6) Later, Save the Method
82. I want to set up a selected-ion-monitoring (SIM) method for one compound using isotope dilution on a 6890/5973 with a purge and trap. There will be 6 m/z values in the group all between m/z 43 and 96. Because of the narrow m/z range, should I do a more tailored tuning for this analysis and what should this tuning involve? (id=118)
First make sure that when you enter your SIM ions and dwell times that the scan-cycle time is about one second or just a little shorter, depending on your GC peak width. Wider peak width can have longer scan-cycle times. You need to have about 8?10 data points (scan cycles) to properly define the GC peak.
As far as tuning is concerned, you will probably have to meet BFB tuning criteria if you work in an EPA lab. In the tuning section of the ChemStation software, you have a choice to tune to target BFB criteria. If you are not in an EPA lab, use Autotune or MAX Sensitivity tune to increase your sensitivity. After tuning your instrument, you may also want to run a sample with moderate concentrations of all of your analytes where you scan over a range that includes all of your SIM ions; e.g., m/z 40?100 in the example you gave. Look at the data and see what the values are for the recorded mass spectral peaks for the specified SIM ions. If necessary, update your method to include these values. This will improve your specificity and possibly your sensitivity.
83. How do I have the calibration gas valve open during an analysis when using the G1701DA MSD ChemStation? (id=127)
In the MS SIM/Scan Parameters dialog box of Edit Entire Method, selected from theMethod menu, click on the Timed Events. This causes the MS Timed Events Table dialog box to be displayed on top of the MS SIM/Scan Parameters dialog box. Select Valve from the dropdown menu for Event Type. This results in a Parameter 1 and a Parameter 2 selection with dropdown menus. One of the selections (only one selection if you do not have other valves configured) Parameter 1 is Calibration valve. Select On for Parameter 2. You should enter the time from the start of the analysis until the calibration valve is to be opened in the Time entry area. Then click on the Add. You should also enter an Off time which should be later than the On time. After you have entered the ON and Off times, Select the OK button to close this dialog box and return to the MS SIM/Scan Parameters dialog box.
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