Open source Chemstation alternative

[eselmeister]

The new release 0.8.0 "Dempster" has been published!

http://www.openchrom.net/main/content/downloads.php
http://en.wikipedia.org/wiki/OpenChrom

There is an enhanced quantitation support available now! Documentation and demos will follow.

[rp18]

I'm trying to use Openchrom together with Profilab software and a simple Labjack A/D converter for a low cost data acquisition solution for our HPLC's. I now can generate ASCII data files (like CSV files, signal vs time, can open them in Excel), but cannot open them.
I've renamed them to .xy, but get an error message when trying to open. I didn't find a .xy plugin (like the Agilent FID one).
Any ways to use Openchrom in this way?

[eselmeister]

The format of the xy files is the following:

retention time in minutes TAB intensity

The extension must be .xy.
You can also contact us under:
http://www.openchrom.net/main/content/contact.php

[rp18]

Thanks!
So I have to change the data format. Profilab has a fixed file format AFAIK, so maybe I'll write a little converter.

[rp18]

OK, saved a file, renamed to "filename123.xy", replaced ";" by tab, replaced "," by ".", opened in Openchrom.

Now all I can do is watch; peak detection, reporting etc. is not working.
If I select a range for manual peak detection, is does not appear in the lower left window. What am I doing wrong?
(btw. - is there an Openchrom forum? )

[U$100autosampler]

Can it control PAL autosampler?

[tlahren]

As far as I understand it, the software is for post-analysis data processing only. Will not control instruments.

[Klinge42]

OK, saved a file, renamed to "filename123.xy", replaced ";" by tab, replaced "," by ".", opened in Openchrom.

Now all I can do is watch; peak detection, reporting etc. is not working.
If I select a range for manual peak detection, is does not appear in the lower left window. What am I doing wrong?
(btw. - is there an Openchrom forum? )

There is a workaround to use OpenChrom to handle xy-data (peak detection etc.). You need to convert the xy-files into "fake" MS data (with only one mass trace) saved as csv-files. The format of readable csv-files is described here http://www.openchrom.net/dokuwiki/doku.php?id=csv_.csv .

[rp18]

Thanks - I'll try. But I don't understand why I can open csv files but not being able to do anything with it.

I've tried Chromulan which works well but it's like working with Windows 3.11
The import filter on Chromulan has a lot of settings and works great. That would be a nice thing for Openchrom.

[Klinge42]

Thanks - I'll try. But I don't understand why I can open csv files but not being able to do anything with it.

I've tried Chromulan which works well but it's like working with Windows 3.11
The import filter on Chromulan has a lot of settings and works great. That would be a nice thing for Openchrom.

OpenChrom was initially only focused on MS data. In the next upcoming release an extensive support of xy-type data is planned, without workaround.

If you convert your data into the csv-file format described under the link posted previously, you will be able to do integration etc.
What you have to take care of, is that the column headers are exactly as described, the RT milliseconds are integers, the RI column is filled with zeros as double values (0.0) and all values are separated with semicolon. For this workaround the intensity values have unfortunately to be non-negative. You may give the intensity column any positive integer name (e.g. 18, according to mass trace 18).
The created csv-file may then be opened in the MSD perspective. The conversion of xy-tables to the appropriate csv-file format could be done batch-wise using code in MATLAB, R, KNIME or other self-written scripts/workflows. If you run into problems contact us via the openchrom-site and send us some test-files. I have a KNIME-workflow ready for the batch-conversion.