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Category: LC, LC/MSD ChemStations

Records returned: 35

LC, LC/MSD ChemStations

1. How do I remove the Agilent LC or LC/MS ChemStation software from my computer? (id=14)

The "Asterix" or "LeoChem" software from Agilent runs the HPLC, LCMS and other anaytical instruments, but not the GC/MS. There is no "uninstall" feature, so you need to delete it yourself. You need to (1)remove files and directories from the computer's hard drive, (2) edit the WIN.INI file, and (3) remove shortcuts to the software from your desktop and the "ChemStations" menu item from the START/PROGRAMS group.

First, make sure that you back up or copy your essential ChemStation methods or method.m directories, and data or data.d directories. The ChemStation can be configured to store these directories almost anywhere on the hard drive, so it's up to the individual to locate them and store them before we remove the ChemStation software. There may be other files you need to save, such as sequence or batch files.

Next locate and delete the directory \hpchem\. Be sure to delete all the files and subdirectories in the \hpchem\ directory. Use any tool that you like to delete files, such as "Explorer" or "My Computer." The ChemStation can be configured to install the \hpchem\ directory on any local hard drive, but it's usually on the "C:\" or "D:\" drives.

The next step is tricky. You need to remove from the WIN.INI WINDOWS system file all of the [PCS] sections. There will be the main one, called [PCS], and then an additional section for each instrument that you have configured for your computer, such as [PCS,1] for instrument number one, and [PCS,2] for instrument number two. Use "SYSEDIT" to edit WIN.INI. Press the "START" button, and then select the "RUN" menu item, and then type in SYSEDIT, and finally press the "OK" button. SYSEDIT lets you easily edit AUTOEXEC.BAT, WIN.INI, and SYSTEM.INI. It's a text editor. Be careful and do not edit lines that you are unsure about. See below for the lines on the [PCS] section that are removed for a typical LCMS computer:

[PCS]
Path=C:\HPCHEM
links=1
link1=HPBSICL,1,7,0,3
USEPOLL=YES
Devices=1,2
Device1=1,20,SMARTCARD
Device2=1,15,68GC
Instruments=1,2
Applications=HP-GCMS,HP-LC,HP-MS
ReportFontName=Courier New
ReportFontSize=10
REV=9.01.00
CORELOWMEM=0
WIN2K=1

Finally, you need to remove the ChemStation shortcuts from your computer DeskTop, and you also need to remove the "ChemStations" menu item from the "START/PROGRAMS" folder. Just drag any ChemStation shortcuts on your DeskTop to the recycle bin to remove them. To remove the references to the "Chenstations" group in your Programs folder, it all depends on how your computer is configured, and who is logged on at the time when you are removing them. I always use a technique that's doesn't care about any of that however. Using EXPLORER, on Windows 2000, I find on the C:\ drive a folder called "Documents and Settings". Inside I find another folder called "Start Menu". Inside Start Menu I see a folder called "Programs." When I open up Programs, I see a folder called "ChemStations." Right click on it and then press the "Delete" option to remove it, or, view it in the right pane, and then drag it to the recycle bin. Note that this example is for Windows 2000. Using older versions of Windows, look for the "Profiles" folder, and in there look for "Programs" and then "ChemStations". Remove ChemStations from Programs. This removes any launch icons which should be removed since there is no ChemStation software to launch anymore.

There are various reasons why you need to remove the ChemStation software. Usually, an Agilent technical person will suggest that you remove it, and then install it again when severe, unexplained problems occur, but note that this is a drastic approach. Installing the ChemStation software means that you need to run all the various Configuration steps again. So, make sure to have these settings stored somewhere before you remove the software if you intend to operate and instrument again on this computer.

2. How do I create a text file that lists the time/abundance data pairs for a chromatogram on the Agilent HPLC ChemStation? (id=15)

This is easy and fast, although it probably can not be automated. To create a text file, or Comma Separated Value (CSV) file that lists the time/abundance data x/y pairs, go to the Data Analysis view of the ChemStation. Load in a signal, or data file. Under the "File" menus you should see an item called "Export File". Click on this with the mouse, and then click on the selection that says "CSV". Now you should see many choices to look at. You can create a CSV file that represents the integration results, raw data pairs, calibration table information etc. You can create your own name and location of the CSV file, or use the default name and location. Be sure to select the "Full" menus under the "View" menu selection in order to see the "Export File" menus. NOTE: most labs need to automate this process, and that is accomplished by usning the macro language that comes with the ChemStation

3. How do I create a text file or comma separated file (CSV) that represents the mass/abundance pairs of a mass spectrum for the Agilent LC/MS ChemStation? (id=16)

This is easy and fast, although it probably can not be automated. To create a text file, or Comma Separated Value (CSV) file that lists the mass/abundance data x/y pairs, go to the Data Analysis view of the ChemStation. Load in a signal, or data file. Use the ChemStation GUI toiols to select a mass spectrum. Next, Under the "File" menus you should see an item called "Export File". Click on this with the mouse, and then click on the selection that says "CSV". Now you should see many choices to look at. You can create a CSV file that represents the integration results, raw data pairs, calibration table information, spectrum, and "Active Graphic Window." Do not use "Spectrum", but instead use "Active Graphic Window." You first need to make the mass spectrum "active" by clicking on the area with the mouse. You can create your own name and location of the CSV file, or use the default name and location. Be sure to select the "Full" menus under the "View" menu selection in order to see the "Export File" menus. NOTE: most labs need to automate this process, and that is accomplished by usning the macro language that comes with the ChemStation.

4. How do I interface the LC or LC/MS ChemStation with Microsoft ACCESS? Can I use the ChemStation database macro commands? (id=25)

The best way to interface information between any database and the ChemStation is by using a combination of two technologies. First, you need to know the ChemStation macro language inorder to gather information to send to ACCESS or receive information from ACCESS. For example, you will create a text file, a comma separated text file (CSV), and an INI file using a macro. Second, you need to know a programming language that will let you create a "driver" to send and receive information to and from ACCESS. The driver is typically a Windows executable program written using something like Visual Basic, Delphi, C++, or one of the new technologies from Microsoft that utilizes the .NET, such as C# [C Sharp]. The executable will read the text file that you created with the macro language, and then place the information from the text file into the ACCESS tables. In a similar fashion, to receive information from ACCESS, you need to write a driver that will ask ACCESS for data, create a text file from it, and then a ChemStation macro can read the text file and place the data into variable names, or even create a sequence file. In general, the macro will launch the executable using the EXECNOWAIT command.

5. Is there any way to utilize the LC/MS ChemStation RS-232 macro commands? How can I send and receive ChemStation data over the RS-232 port? (id=26)

The best way to utilize the RS-232 port to send and receive ChemStation data is to use the macro commands to prepare the data, and then write your own Windows program that will talk to the RS-232 port to send and receive the data. Most likely, you will use the macro language to create a text file, such as a file containing lines of x,y data points, and you will use the Windows program to initiate the RS-232 connection, read the text file, and then send it down the port. The macro language RS-232 commands are not too reliable, and are not documented well.

Should you be interested in using an RS-232 port to operate an Agilent hardware component, you will need to contact Agilent for the proprietary documentation, and price.

6. What is the "sendmodule" macro command useful for? Can I use it to write my own macros to operate hardware units such as the LC autosampler and contact closure board? (id=27)

There are proprietary macro command strings that are used with the "sendmodule" macro command that will allow you to operate hardware units such as the autosampler and the contact closure board. You will have to contact Agilent for the documentation, and price. You will also need to be proficient with the ChemStation macro language. This is useful if you need to enhance the ChemStation, for example, by writing custom macros with the sendmodule command that use the contact closure board to send contacts out to third party hardware devices. It is useful to coordinate devices this way that work together to perform a complex analysis using non-Agilent and Agilent supported devices.

7. I use the LC/MS ChemStation Data Analysis software. I look at mass spectra in a bar graph format. All the mass spectral peaks are floating above the abscissa of the display. This may be fine for profile data, but is not for bar graph data. How can I prevent this ridiculous display? (id=50)

There is no way to stop this in the LC/MS ChemStation. You can look at your LC/MS data using the GC/MS ChemStation Data Analysis. This will require you to purchase the GC/MS Data Analysis software from Agilent. The GC/MS Data Analysis software does not float the mass spectral peaks; however, this software does not allow for the display of mass spectra in a profile mode.

8. How can I control how the LC/MS MSD ChemStation prints, such as landscape versus horizontal? (id=56)

From the "TOP" view of the ChemStation, under the "File" menu selection there is an item called "Printer Setup." Use this to choose between landscape and horizontal page printing. You can also reverse the order of printed pages here.

9.

How can I change the default paths, or, where the data files will go, or where the ChemStation goes to look for sequence files or methods?

First, you need to turn off all ChemStation sessions. Then you need to run the ChemStation Configuration Editor. On later computers, you can access this from the Windows START button. Go to Programs, then ChemStations, then Configuration Editor. You should see a box for each instrument that the computer is operating. Click on the box for the instrument that you are interested in making changes to. BE CAREFUL HERE WITH YOUR CHOICES! Next, under the Configuration menu item, select PATHS. A dialog box will appear. Use this to change settings, for example, the root directory or root folder for all your data. Save the changes, turn off the editor, and then start up a session. You should see you changes.

10.

How can I start or stop the ChemStation from integrating when I load in a data file?

From the Data Analysis View of the LC ChemStation, you load in a data file or use the "Load Signal" menu item under the "FILE" menus to laod in a sample. A form pops up. At the bottom there are two checkmarks. One is "Integrate after load", and the other is "Integrate and print report after load". These allow you to control what happens when you load in data. To make your choice part of the method and reproducible, you need to Save the method after you make the changes.

11.

How can I store manual integrations and reproduce the results?

The best way to do this is by using the Batch software. This is found in the Data Analysis View. This works with data collected as part of a Sequenced run. The data needs to be processed by a calibrated method too. Once you have taken care of these details, you can use the Batch menu items to view the data, the baselines, and manually integrate the baselines, thus, changing the results, and, the manual baselines are stored with the Batch so you can reproduce them.

12.

How can I copy a chromatogram or spectrum to the clipboard so I can paste it into another Windows program, like Word or Excel?

In the Data Analysis view of the ChemStation, under the "Graphics" menu items there is a selection called "Copy to Clipboard." First, view a chromatogram or spectrum so you have something to copy, then use "Copy to Clipboard." You will need to select which graphics window you want to copy. Then, immediately go to another Windows application abd paste it in.

13.

How can I annotate a chromatogram or spectrum?

Once you are looking at the chromatogram or spectrum that you want to annotate, use the menu items under the "Graphics" topic and select the choice called "New Annotation." You will see a mouse pointer that looks like a vertical line. Move it to where you want the annotaion text to appear on your graphic. Then click the mouse. A dialog box will appear where you can enter text. Enter text and see what happens. The text will go where you clicked the mouse pointer. Be sure to play with the "Options" button in the dialog box. Also, experiment with the other annotaion choices under "Graphics."

14.

I like to use the autointegrator, but I noticed that it's very slow. Can I speed it up?

In the Data Analysis section, under the "Integration" topic, there is a choice called "Autointegrate." It can help you by selecting best integation parameters, but it's slow. You can speed it up, and you may want to if you use it all the time. NOTE: this can be a tricky maneuver, so pay close attention. There is a macro or text file in the \hpchem\core\ folder called "autoint.mac." There are about seven or more lines in this file that are "sleep" commands, for 3 seconds. You can edit this text file and comment out all the "sleep 3" macro commands. To do this, open autoint.mac in Notepad, locate all the sleep commands, and put a bang sing in front of them. For example, change this: sleep 3 to this ! sleep 3 Then save the file. The next time you turn on the ChemStation session, autoint.mac will be loaded, and the Autointegrate function will run faster. This is NOT an Agilent supported solution, and it WILL violate GLP procedures, but if that's acceptable to you, then there should not be a problem.

15.

Can I import sample information and make a sequence file from data stored in Excel?

Yes. Agilent supplies a template file hpchem\1\sequence\ def_std.csv to help you do this. You need to create a CSV or text file from Excel, not an XLS or propietary format file. Look under the Help menu and then search under topics for "CSV." It is explained well.

16.

What type of graphic file formats can I create from chromatograms and spectra?

The ChemStation creates black and white GIF files as part of the .HTM report style, as found in the "Specify Report" section of Data Analysis. These GIF files are graphic representaions of the report and are widely seen in Internet browsers. These ChemStation GIF files contain text and graphics on the same plate. There also is a .WMF graphic file format that just contains the chromatograms, and in color. WMF is the Windows metafile format. These can be imported into Word for example as a picture. Additionally, you can copy any graphic to the clipboard as a BMP file format and then paste into another Windows program manually. Look under the "Graphics" menus in Data Analysis.

17.

Can I load the LCMS ChemStation software on Windows XP?

No, you can not load the LCMS ChemStation software on Windows XP, as of version A.09.01. Look for a new release coming out from Agilent that will support Windows XP.

18. Where can I get written material on creating macros for the LC(MSD) ChemStation? (id=119)

The LC (MSD) ChemStation is actually one of a family of ChemStations. The member of this family that supports the LC(MSD) is called the Agilent ChemStation, and it's underlying structure supports GC, LC, LC-MSD, CE, and UV-Vis. Macro writing is one of the advantages of the various members of the ChemStation family. However, unlike the Agilent GC-MSD ChemStation, the Agilent ChemStation Macro functionality may require a significant investment in time to master. Because of this and the issues of support, Agilent has traditionally not been that enthusiastic for customers to have access to this documentation. This is somewhat evident by the lack of any Agilent ChemStation Macro classes.

However, the UV-Vis group decided that a general document regarding the Agilent ChemStation Macro functionality was valuable and created one. As the LC(MSD) ChemStation functionality is based on the same platform; therefore, there was no need to write more than one document. At one time, the document was included in the software CD set. Depending on your revision, you may find this documentation on the installation CD. It is also available from the literature section of the Agilent Web site.

As you turn your attention to learning and writing Macros, you may want to consider the alternative of working with a knowledgeable consultant to write you Macros. You may find that this is the quickest, most efficient, and cost effective way to proceed. Of course, ChemUserWorld can offer that consultation and service.

19. I have the LC/MS MSD ChemStation and the NIST MS Search Program v.1.6d. I want to build my own library but cannot figure out how to get my spectra into the NIST MS Search Program. There does not appear to be any menu items that will allow me to send spectra to the NIST Program. (id=124)

If all the components are installed, the bottom three options on the Library menu displayed by selecting Library from Spectra on the Main Menu Bar should begin with MS and are self-explanatory. In order to make the NIST MS Search Program?s interactive button bar available in the LC/MS MSD ChemStation, you must first load a library of UV spectra. You do this by one of two ways. The first way is by selecting Spectra from the Main Menu Bar and then selecting Library from the Spectra menu. Select Open Library from the Library menu. The second way is to click on the Load Library button (next to last button from the left on the horizontal button bar). Either will result in the Open Library File dialog box being displayed. Select the DEMODAD.UVL file even though you have no interest in searching a UV library. Then click on the OK button in this dialog box. A vertical button bar will appear on the left side of the display. The last two buttons are associated with the NIST MS Search Program. The top button is used to initiate a spectrum file and add displayed spectra to this file. Spectra are added each time the button is clicked. This will continue until the bottom button is clicked, which will cause the file to be closed, and the NIST MS Search Program will be started or brought into focus if already running. The spectra will then be loaded into the NIST MS Search Program by overwriting or appending the current contents of the Clipboard Window (v.1.6 or v.1.7) or Spec List (v.2.0). Whether the current contents in the NIST MS Search Program are appended or overwritten is determined by the settings in the MS Edit Defaults dialog box displayed by selecting the Spectra menu, then selecting the Library menu followed by selecting MS Defaults at the bottom of the Library menu. If you do not have the three MS items at the bottom of the Library menu, check to see if you have the NISTMS.INI file in the \HPchem\MS (or \MSDchem\MS) folder. If this file is not present, you will need to create it. Create the NISTMS.INI using Windows Notepad. The contents are shown below. Be careful that Notepad does not add a .TXT on the end of the file name; e.g., NISTMS.INI.TXT. You may have to set Windows Explorer so that it DOES NOT "Hide file extensions of known file types" (Tools\Folder Options\View from the Main Menu Bar of Windows Explorer).

[General]
AutoParms= /INSTRUMENT /PAR=2
NistDirectory=D:\NIST02\MSSEARCH (path for NIST MS Search Program)
Program=NISTMS$.EXE (for NIST MS Search v.2; NIST$.EXE if NIST v.1.6 or v.1.7)
ManualParms= /INSTRUMENT
NominalMass=Sum
ClipBoard=Append

C:\HPchem\HPNIST.TXT or C:\MSDchem\HPNIST.TXT

20. I am using the LC/MS MSD ChemStation. I upgraded my NIST MS Search program version 1.6d to the new version 2.0; however, whenever I call the program from the commands within the LC/MS ChemStation, I still get v.1.6d. Agilent cannot help me. (id=125)

You need to change the contents of the NISTMS.INI file that is in either the \HPchem\MS or the \MSDchem\MS folder. Open the file using Windows Notepad. You will see the following text:

[General]
AutoParms= /INSTRUMENT /PAR=2
NistDirectory=C:\NIST98\MSSEARCH
Program=NIST$.EXE
ManualParms= /INSTRUMENT
NominalMass=Sum
ClipBoard=Append

LC, LC/MSD ChemStations / Data Analysis

21. Why are there underlines under specific letters of the selections on the Menu Bar? (id=100)

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.

22. What is a mass chromatogram? (id=101)

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.

23. How can I annotate a chromatogram? (id=104)

You can annotate a chromatogram very easily. First, make sure that the FULL menus are selected. Do that by using the VIEW menu items. Next, under the GRAPHICS menu selection in the Data Analysis view there are annotation menu items that allow you to annotate a chromatogram. Click on "New Annotation" and when you place the mouse cursor over the chromatogram it will assume a line shape. Place the cursor where you want your annotation to be and then click the left mouse button. A dialog box will next appear. Type your text into the edit field and then press the "OK" button. You should see your annotation on your chromatogram. These same tools allow you to move and delete annotations. You can also control the font. Experiment and have fun.

24. How can I annotate a mass spectrum? (id=105)

You can annotate a mass spectrum very easily. First, use the spectrum tools to obtain the mass spectrum that you want to annotate. Next, make sure that the FULL menus are selected. Do that by using the VIEW menu items. Next, under the GRAPHICS menu selection in the Data Analysis view there are annotation menu items that allow you to annotate graphics. Click on "New Annotation" and when you place the mouse cursor over the mass spectrum it will assume a line shape. Place the cursor where you want your annotation to be and then click the left mouse button. A dialog box will next appear. Type your text into the edit field and then press the "OK" button. You should see your annotation on your mass spectra. These same tools allow you to move and delete annotations. You can also control the font. Experiment and have fun.

25. With the newest ChemStation software A.09.03 coupled to the Chemstore B.02.02, is it possible to produce overlaid chromatograms, without recalling datafiles back to ChemStation from Chemstore and thus producing an amended version? (id=116)

Chemstore was designed as a data management (review/ approval/ GLP) application. Information, charts, and other processed data can be displayed in various ways, including overlays. However, with regards to chromatographic data it assumes that the raw data processing and re- processing is/was done at the application ChemStation. This has been a long requested feature in Chemstore. To the best of our knowledge this feature is not in B.02.02 Chemstore.

LC, LC/MSD ChemStations / Macro Language

26.

Where do I begin if I want to learn how to write my own macro for the LC LC/MSD Agilent ChemStation?

There's a macro class offered by Agilent, somewhere in the east coast, so check their class schedule to see if the content will be able to help you. ChemUserWorld.com also teaches on-line classes on macro programming.

27.

How do you create arrays with the LC ChemStation macro language?

p> You can and you can not create arrays with the LC ChemStation macro language. You need to create a table, like a database table, and you can do that with the macro language. So, if you need an array of x,y pairs, then you would create a table of x,y pairs. It does what you need it to do. These tables hold either text or numbers, and you can hold text in one column and numbers in another, both in the same table.

28.

What macro command shows me what variables, macros, commands, and functions are currrently loaded into the ChemStation's memory?

The "SHOW" macro command shows you what variables, macros, commands, and functions are currrently loaded into the ChemStation's memory. It does a few other things too. Type SHOW at the command line.

29.

How can the ChemStation macro language communicate with other Windows programs?

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.

30.

What debugging tools are available for the macro language?

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. An example is: LOGGING 6,"C:\temp\LOG.TXT",ERASE.

Another useful technique is to place "PRINT" or "SLEEP" commands, or the "ALERT" function, at strategic points in your macro, especially if you have a hint where the error is occurring.

31.

What type of error handling techniques are there with the macro language?

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.

32.

What are macros, how do I make them, and what are they used for?

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.

33.

Are there any variables that the ChemStation creates that I can use in my macros?

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 "SHOW" command.

34.

Can I use my VB editor to write macros?

Yes you can use any text editor to write Chemstation macros. Note that a word processor is not a text editor, like WORD or WORDPERFECT.

35.

I am looking at the variable names in the ChemStation using the SHOW command and see that there are many that start with the underscore ("_") character. What is the significance of the underscore in their name?

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.