Chromatography Forum

We use Agilent's Chemstation (LC-MS) and are currently on version B-03-01 SR1. We'd like to use XCMS to process data, running in R for Windows.

XCMS requires .cdf or mzXML files. Agilent's built-in converter is giving us nightmares. Firstly, it can only convert files with 8 or less letters in their name, although the newer versions of Chemstation, when using prefix+number file naming, will only produce filenames with 9 or more letters, so we have to change all the file names before the converter will work.

Secondly, once we've done this, XCMS crashes when we open the Agilent cdf files ("The R for windows GUI has encountered a problem and has to close"). XCMS in R for windows will open cdf files generated on other instruments.

I'm scared that the developers of XCMS and Chemstation may be at cross-purposes in their understanding of cdf format, and we'll get caught up between two groups of people declaring the other to be at fault, or they'll both tell me (politely) I'm too stupid to use XCMS, which is quite possibly true.

Has anyone else encountered this problem? We'd be very grateful if anyone knows a way round it.

Not sure I followed you completly and I never had to export MS data but this might be a clue?

Unless someone really knows have you tried to talk to Agilent directly?

I need to import or export AIA files, how can I create or export NetCDF files?
This feature is built into the LC/MSD ChemStation software, all you need to do is ensure Full Menus are active in DataAnalysis. Select View then verify the last menu listed reads 'Short Menu'. This means we are in Full Menus, this item function as a toggle switch. Next select File-Import File or File-Export File then select the AIA File selection. Also note the other file types support with this feature, CSV and DIF files

A similar problem occured a few years ago with a previous ChemStation package. The data files were exported in CDF format into a third party program, and the Agilent files converted fine, but files from another package would not import correctly. When the programmers at the third party software disabled some of the changes that had been made to make Agilent files import and used a "pure" cdf import filter the other files imported correctly. So Agilent does have some history of using a modified CDF format.

Thanks both! Ron, you may have hit on what's going on. If Agilent are using a modified version of .cdf, it might well be confusing xcms. We have some limited access to xcms's developers coming up in a few weeks' time, so I can find out from them whether they have any way to deal with weird .cdf formats. In the meantime I will grit my teeth and phone Agilent, and see whether a small lab can influence a big company sufficiently to find out exactly what they're doing with their cdf. If need be, we'll have a look at it directly.

Just in case anyone digs this thread out in the future:

Agilent have now fixed this issue with a patch that applies to Chemstation B.04.01 SP1.