Usability and annoying things in Chemstation

[Cmdr Keen]

Hi,

last week we got our fast scan upgrade for the 6890/5973N and with it came a new WinXP-computer which replaced the old NT4 machine. With this came the latest version of ChemStation.
Up to now I used the Chemstation only for getting the raw data, all quantitation and MS search was done by exporting into AIA-format and working with the software of another machine.

Now, after the upgrade, I want to work with chemstation again but there are several annoying things that don't make life easier. I'm wondering if I'm too stupid or Chemstation is... normaly I won't consider me as a PEBCAK
Maybe one of you can give me hints or workarounds to some of the following points:

1) This is rather cosmetical: When I click onto a peak and let display the mass spectrum, the masses are shown with 1 digit after the decial point. From a scientific or technological point of view this may be progressive but I'm used to integers and have a trained eye on integers. Thus it's more difficult for me to recognize a common spectrum without library search. Is there a way to setup the mass number view? Maybe even in some configuration file?

2) Most chromatograms are screenings of unknown material or unknown contaminated materials. So I'm not working quanitative in most cases but I have to have a close look to every peak, even those with low integrated area. Often huge peaks are not important to me 'cause their existence was expected and is not of interest, but a contamination (a small siloxane peak e. g.) is of major importance.
The autointegration mechanism of chemstation is not very useful for this situation because I won't get the peaks of interest with threshold setup and it would take a lot of time to integrate all peaks of interest by timed events. Only way here seems to be manual integration. So my question is: Is there a way to securely store manual integrations to the data/method file, maybe including annotations? They are important for me and the customers because concluding "substance a and b is included" doesn't make them believe, I have to show it in the chromatogram by a text or number annotation.

3) When I make annotations (well aware that they will be not stored [why ever]) and I want to copy the annotated chromatogram to the clipboard, there are several possibilities in the software. So far so good. But goodness ends if I paste it in excel, word or a graphic processing programm. The Chromatogramm is there, the annotations too, but they are not at the same place as they were originally. There's always a more or less big shift in x or y direction of the axis. Apart from that the font for the abundance and time axis looks awfully distorted. I can correct that by enlarging the chromatogram into one direction but is this the only solution?
I know, I could make a screenshot in Chemstation, but it's annoying to edit that screenshot everytime in gimp and cutting away everything that hasn't to do with the chromatogram.

4) is it possible to display a chromatogram with only (manualy made) annotations WITHOUT retention times? Displaying retention times is confusing non-chemists and gives too much information about analysis to the competitor...

5) In the software I used up to now (Shimadzu) it was possible to integrate the <selectabe number> highest peaks in the chromatogram. Is there a similar possibility in Chemstation? Or is there a (theoretical possible way) to write a macro performing that task?


6) Are there any chemists out there who don't do routine analyses and perform screenings? Am I the only person with that problem? I feel a little bit lost. I'm well aware that Chemstation was not designed for such usage but after decades that software exists I think it should have been achieved by agilent to design the software into that direction as well - not only since screening is wide spread too in the meantime...


Thanks for any hints,

Commander Keen

[chemstation]

Hi Keen,

IMHO these would be my responses:

1) For non-integer values particularly if you are use to seeing 194 and now see 193.9, it is annoying, I have spoken with Agilent Techs, to see if they can know how , no luck
Though viewing spectra with AMDIS, has the integer values
(or use the Old PC with older version software to Data analysis file)


2) I suggest a two fold approach:
a) AMDIS will find threshold peaks, even those co-eluting

b) Have you used Qedit, with the opinion, with "draw chromatogram with labels"
that way, the chromatogram is instantly annotated, and you can process a batch of samples, without have to type in the same information, and no errors in retention time positioning nor typographical mistakes.
plus by using Qedit, that information is stored in the data file directory, you need to play around as reprocessing the data with a different method, will by default, display the latest processed data method.

3) Humm... never noticed that before, I usually print to a PDF ( Has Colour ) eg PDF995 (free) , and use the 'snapshot' function to copy and paste, or store the PDF with the data file for retrieval. WYSIWYG

4) Yes, see 2)b)

5) Select integrator to RTE Integrator, then MS Integration parameters , maximum number of peaks in Output Square.

6) I feel your pain, I wanted that too, Now I have dual monitors, AMDIS on one, and Chemstation on the other. I use AMDIS to hunt peaks for me, and Chemstation to confirm and printout results.
I wrote a Chemstation macro to find the retention time of peak found in AMDIS, and show the Mass Spectra,
I also wrote one to zoom in on the area, but that was based on integrating the TIC. not useful for co-eluting/ non integrated peaks of interest.

end of hints

never heard of PEBCAK before, will use it in the future

Alex

[Cmdr Keen]

Hi Alex,

now my fears concerning chemstation tend to distinguish...
The tip with AMDIS is great. I always knew about the existence of this software but in the past I just considered it as a free by-product of NIST with only academic use and never paid attention to it.
You're right - identification with AMDIS ist quite time-saving. This week I had to look for phthalic acid esters in 8 chromatograms, so I just set the cursor to mass 149 and it was done in seconds.
Now I only have to find out how I can search in my NIST 2002 from AMDIS directly. Would be great if this works, but right now I didn't have time to try and setup.

With the help of gimp chromatogram cosmetics can be performed quite well with the effect of learning more about gimp which surely is useful for other situations as well.

Thanks for your tips! It was great help for me!

[chemstation]

to finish off your wish

to search NIST02 directly from AMDIS, is as follows:

Select Analyse

Select Search NIST Library

Choose the Parameters and Click on Analyze


I usually set:
- Min Probability to 60%
- turn off Build Combined results, as I'm only interested in NIST Library, not my own library.
- select "all above threshold", or, as mentioned in you posting for a want, you can also select only X largest peaks.


for you 149 extracted Ion chromatogram, in Chemstation it is possible to display an extracted on a series of data files by:
Tools -> Overlay Chromatograms

select Selected Ion , then Click OK

type in 149, and select the files you want to process, Click on Process
and there you have a EIC of 149 Ions, I then print the chromatogram to PDF and look at that, as you can't choose which file to display the Mass spectra for.

If you have Chemstation version E, you can click on the Icon with the two peaks and the letters m/e, and type in 149, then click OK to re-display the 149 EIC. otherwise click on chromatogram -> Extracted Ion Chromatograms... for the sample display.

Whilst Gimp, is good picture editor, there are other software printers eg Zan printer, where you print it out as a BMP,Tiff or JPEG etc..., that you can import directly in word.

Alex

[Cmdr Keen]

Hi again,

many thanks for your hints. May I ask you for another one?

AMDIS ist behaving strange...
I can load a chromatogram (.D-file) from chemstation and it is displayed correctly. So far, so good.
If I want to search for it in NIST, I click in the mass spectrum on "NIST Library" --> "Go to NIST MS Program". That causes the error message: "Unable to write spectrum".

Is this normal? I just want to look up the spectra of unintegrated peaks in NIST, peak by peak.
I can solve this problem by clicking on "Analyze GC/MS data" in the "Analyze" menu. After this operation, NIST comparisons are possible.

BUT: After performing that, the program does something strange to the spectra: It substracts 1 mass unit of each mass peak. So my substance Squalene (masses 69/81) is displayed with masses 68/80 which of course makes NIST find nothing of use.

Is there a simple thing I did not recognize? What could be wrong? Or is there a easier way of comparing mass spectra with NIST?

Greetings from a despaired
- Cmdr Keen

[chemstation]

Hi,
The "Unable to write spectrum", is normal, as AMDIS hasn't de-convoluted any spectra until it is run, so can't write a null string to search.

Does AMDIS display the masses as 69 and 81?, as I am wondering if this maybe an integer rounding issue?.
Eg if in Chemstation, the '69' ion, actually reads a mass of 68.7,
then AMDIS may round down to 68, so NIST searches for 68.
(I have tested for 68.9 as seen in Chemstation, which is shown as 69 in AMDIS and 69 in NIST. I could not find a xx.7 ion to test)

Other wise it usually works perfectly.

Alex

[Cmdr Keen]

In the chemstation window the masses are shown as 68.8 and 80.8.
If I load the file into AMDIS without any further action, it shows 69 and 81.
If I run the "analyze data" it ...
... as well shows 69 and 81

hmmm...

it didn't yesterday, I'm absolutely sure and now perplexed.

Well, never change a running system - as long as it runs like it does today.
I'll report if the error appears again and I can replicate it (also after restarting the system).

Thanx,

- Cmdr. Keen

[Cmdr Keen]

Now after two days of support lines I have found the solution and reason for the strange behaviour of my mass detector.

The problem was: Masses are not shown as even numbers in chemstation (e. g. 206.6 instead of 207 for cyclic trisiloxane).
The reason: The fast scan upgrade makes the device not stay long enough on one mass to record it precisely. We even tried to adjust the mass axis manually but it showed no effect.
The solution: Reset the device to "normal scan" instead of "fast scan". Of courst this results in a loss of sensitivity but it works again.

The result for me: If Agilent isn't able to cope with faster scan rates properly, why do they sell a fast scan upgrade though...?