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Knowledge Base Results
Category: MSD ChemStation / MS Libraries/ Databases
Records returned: 25
MSD ChemStation / MS Libraries/ Databases
1. 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.
2. 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:
3. 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".
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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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13. 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.
14. 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.
15. 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
16. 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
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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
25. 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.
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