Chromatography Forum

Wondering if anyone knows if it is possible to convert the data signal (TIC) from an Agilent GC/MS (5971/G1800) from the HPIB to an analogue output? Have not found any information on what data format is used etc from the MS to Chemstation. Would appreciate any help as I would like to import the TIC-trace to a software for EAD (electroantennogram detection) that normally is used with an imported FID-signal (from the analogue output of the GC, 0-1 V). Know of people doing the opposite, importing the EAD-signal to Chemstation via an analog to digital converter, but would like to use the EAD-software if possible. Many thanks, Bjorn

It has been a few years, but the data format for the ChemStation data was available in the ChemStation manuals. I don't remember if these were the manuals for the Pascal ChemStation or a later version. The record has added fields to accomidate some of the newer information, but for the basic GC/MS run, the information you want should be in that first part of the record.

So, if this is not help, let me at least offer encouragement. And, it may be worth looking through the Agilent manuals on the website to see if the information is there.

Hi Bjorn,
Can your EAD software accept other file formats (what is the name of your software by the way?),
As people who want the TIC in excel, for example, usually export the TIC into a text file,
and load the text file into excel, and use the XY graphing function to recreate, and manipulate
the TIC.

As the .ch file format, that is generated by chemstation, is in a proprietary format unfortunately

Does the EAD software specifically look for the .ch file, or does it import it directly from Chemstation?

Alex

Thanks guys! We are using Syntech's software for EAD. My dream was to be able to read the TIC data direct from the MS, i.e. "de-code" what's going on through the GPIB cable, by a "listening" converter to an analogue output or something like that. When running old school FID/EAD, the FID analogue signal (0-1 Volts) is connected to the EAD control box and then you see the FID signal and the EAD signal simultaneously online on the PC. But of course it is interesting to think about converting files afterwards too... the Syntech software produces .ead files...

Hi Bjorn,
I had a quick look at Syntech, and their software at http://gcead.sourceforge.net

I need to understand, are you using the Syntech interface to acquire data from a GC, or chemstation to aquire the data, and the GcEad software to process it.
As a quick look at the software documentation does not seem to indicate that it can import the chemstation .ch files,
Syntech wrote about their old EAD file format, and ASC files and XML in https://gcead.svn.sourceforge.net/svnro ... k/Todo.txt
so you may need a macro to create a custom output,

when you go to open a file does it offer to import .txt files?

Also please note that for GCMS data, the retention times are different for the same compound,
as the MS is under vacuum, and the EAD is at atmospheric,
If you want to align the response you see in the EAD with the MS, there are components that can do that for you ( i.e. microfluidic splitters), but these reduce detection limits.
(I assuming that is why you want to keep the GcEad software?)


Alex

Thanks Alex,
The Syntech software cannot import/export anything as it is (as far as I know anyway). The only input (online data, not files) is from the control box. There are two types of boxes, one connected through USB and the older model with serial interface. To this box (IDAC) the GC output is connected. The reason I want to keep the Syntech software is the very easy manipulation of EAD-data and when it does work it is very easy to use, there is a good noise filter and it produces publishable traces and easy to align traces compensating for different flow rates. I am aware of the issue with different retention times MS-EAD. Have in fact not had a chance to test our system yet since we don't have a control system (insects) at the moment. All I have done is to compare peak area on the MS with and without splitter and measured flow rate at the atmospheric end after fiddling around with diameters and lengths of capillaries. But the difference in RT should be fairly linear, right? If no-one knows of an easy solution I would probably do like colleagues done previously, connect the EAD-output to an analogue/digital converter (think know of a 35900 box) and import the signal to Chemstation. But still curious about the data format from the MS detector through GPIB to Chemstation and if that can be converted to something standard...

Hi Bjorn,
That's odd, that the software should import data files as the link at sourceforge writes it can ???? : https://gcead.svn.sourceforge.net/svnro ... k/Todo.txt,
anyhow, when you choose export wave, it creates a CSV file that can be imported into excel, oddly,
when you go to to import wave files, it only look for .ead files ???? very strange!

But the difference in RT should be fairly linear, right?

"fairly..." is a loose word, eg RT difference at the beginning of run could be 1 minute, towards the end of the
(oven gradient) run could be .2 of a minute, more quadratic than linear.

But an old school Y splitter on the end of the column has been used successfully in the past to counter the change is visocity.

I am assuming you have either version A.02 or B of the chemstation software, as I don't seem to recall being able to get a 35900 box recognised as a detector in later MSD chemstation versions.


To satisfy your curiousity about the GBIP cable, this cable only transmits digital information, As an Analytical Chemist you should remember that the only place you could ever possibly hope to get an analog signal is to
tap into the electron multipler (EM). As the EM only generates electron flow, (the voltage is constant), the amps increase as the number of ions strike the Electron Horn, ejecting electrons at the same potential (voltage), producing a cascade of electrons in the EM

which is when the GCD electronics convert the current (from the EM) into a digital value.
(I'm guessing the reason why you are curious is that the control box is Dual channel, and you want to get an analogue VOLTAGE signal from the MS to tap into instead of new hardware).

Alex

Alex, you are spot on!
The EAD-files have changed a bit over the years. Today the signals are called waves and several waves make up a file or project compared to older versions of the software where every single recorded run made up one file. I am useless at programming so cannot say more than that re the documentation on sourceforge. At the moment we have two systems running, the old 5890/GCD G1800A with its original Chemstation (G1094, which cannot do two detectors) and then a 6890/5973 running Chemstation B.01.01, which supports the GCD as well. As a naive chemist I was curious how Chemstation translates the digital info from the MS to a TIC trace and if that is a simple digital/analogue conversion so that we can plug the HPIB in one end of a converter (say an old HP programmable power supply with HPIB control) and by reading the right pins get a voltage out the other end, but guess it's not that simple?!
When it comes to linearity of the MS vs EAD I'm not too worried and it is easy to control when we have systems of antenna responding to 5-6 compounds all over the chromatogram so we can see how peaks line up and compensate for that when running unknown systems - using a simple SGE VSOS splitter now, the same as we use for FID/EAD and seems to work ok when it comes to flow rates at least (and that is what is reported to be used in literature).

Hi Bjorn,
I'm guessing that as you have access to a 5973, that the 1800A is a standby/screening instrument that you want to add functionality to, as other people aren't using it all the time, is that correct?

original Chemstation (G1094

??? G1094, not G1034 ... Ver C ?

Is it going to be run using sequences, or one sample at a time ?, as short of hardware upgrades, the only solution is I can see is programming, with the danger in doing this is the assigning the wrong EAD to a MS file if run automatically.

Alex

Hi again, sorry it's G1074A, that's the special version for the GCD where you need a password to tune But can run this instrument with Chemstation B as well, have the install discs. Nah, this is an instrument that I brought back to life and is my own little baby, while as you say the other instruments are shared. If we get it to work with the EAD the other FID/EAD instrument will be replaced with this one as a permanent EAD-FID setup.
EADs are run as single samples, you are lucky if an antenna lasts one run and you want to monitor online in order to see possible responses - sometimes you can tell from the behaviour of the baseline of the EAD rather then the "peaks" if there is a response or just noise.
And once again, I am not a computer guy so programming wouldn't be for me I'm afraid, if we are not talking a few lines of macros...
Björn

Hi Bjorn,

G1074... sounds like you probably have a Smart Card II, in the GCD, running Windows 3.1 using a 82335 HPIB card, is the 5890 a Series I or II ?

As A.03 running in Win95/98 should still work too based on http://www.chem.agilent.com/en-US/Suppo ... onRev.aspx


also what is the other "the other FID/EAD instrument" make/model,


Alex

Hi Alex, yes it's the old interface, but upgraded to Win98 The GCD1800A is a fixed combo, basically consisting of a 5890 series II with EPC built together with a 5971 ms but m/z limited to 450. The other instrument is a 5890 series II witout EPC - that instrument has a newish Chemstation (don´t remember exact version, but running Win XP) but without GC-MS option. Also has a 5972-unit that I plan to use to upgrade the 1800 one day.
Björn

Hi Bjorn,
Finally came up with a software work around, unfortunately can not use the GcEad software.
I wrote an Excel / OpenOffice spread sheet that can create a CSV format that can be opened by Openchrom
http://www.openchrom.net/ (need to be connected to the internet to download conversion plug-ins)

Basically steps are follows:
1) export the EAD data to a CSV file from GcEad. eg as EAD1.csv
2) Open the EAD1.csv in excel
3) Copy the column of data into column A of the spread sheet I wrote formulas in.
4) create a txt file, and open in notepad.
5) Copy the data from column F ( I hid columns B to E), from spread sheet I wrote formulas in, into the txt file.
6) save the txt file
7) rename the txt file, so it is now. eg NewEAD.CSV (note that is now a CSV file)
8 ) open up NewEAD.CSV in Openchrom.
9) open Chemstation data in Openchrom.
10) and compare.

To view the EAD data in Chemstation:

11) In Openchromopen, save the NewEAD.CSV, as a CDF, eg EAD1.cdf
12) Copy EAD1.cdf into the GCMS data directory, eg evaldemo.d.
13) Open the pre_post.ini file in the evaldemo.d directory in notepad ,and paste at the end and save: 14) Open evaldemo.d in Chemstation, and it will be a TIC, if software has align functionality it should work.


To view the EAD cdf data in AMDIS:
15) Open EAD1.cdf file, the in the window right click file->open, then change file type to Agilent, and load evaldemo.d.
16) Only click on the evaldemo.d window for spectra, as clicking on the EAD1.cdf file will only give the fake 84 ion.


If you are interested in the Excel/OpenOffice spread sheet that I wrote email me,
N.B. select column headers during all copy and paste functions, so there are no remains of previous data.

What the Spread sheet does:
1) User defined Hz rating, as need to generate RT in milliseconds and minutes
2) ALL voltage values up shifted up so the lowest negative value is now 0, negative values are not plotted in Openchrom, Chemstation or AMDIS when using MS data.
3) Voltages are converted to uVolts, so can actually see discrete values.
4) formats header and data values,
5) Hides rows with no data, so can copy and paste column F directly into a CSV text file.


if 65535 rows are not enough, then need excel 2007
http://excelsemipro.com/2011/04/spreads ... r-windows/
or Open Office.
http://wiki.services.openoffice.org/wik ... er_of_rows


why I as asking about your other equipment, is the theoretical use of recording the values of temperature inputs, as chemstation allows you to store eg oven, detector temp,injector temp, EPC pressure, as signals, (depending on resolution (discrete points) of course),
I doubt that that will pass any OHS risk assessment, Voltages

chemstation
at
gmail
.
com

Alex

nice.

cool