small molecule support for Agilent Chemstation data files

small molecule support for Agilent Chemstation data files dgmccaskill  2019-08-08

Are there any plans to support working with Agilent Chemstation data files (not MassHunter) coming from an LC-MSD single quad system? This might be a small niche, but it would be very helpful (at least for me) in the small molecule arena to be able to work with SIM data from Chemstation using Skyline.

dgmccaskill responded:  2019-08-08

Quick update. I did find a small utility from Agilent that will convert Chemstation files to MassHunter format automatically after acquisition. MassHunter Qual recognizes the file and opens it, and Skyline recognizes the file but when it tries to import gives the following error message (this was a SIM method):

At 1:56 PM:
Failed importing results file 'C:\Users\xxxx\Desktop\001-0101.D'.
Invalid chromatogram ID SIM SIC Q1=407.3 start=0.05215 end=14.9676 found. Failure parsing m/z values.

MS1 filtering was set for counting 1 isotope peak, centroided, 100 ppm mass accuracy.

Brian Pratt responded:  2019-08-12

Have you tried looking at that file in ProteoWizard's SeeMS viewer, or converting with msconvert? That may offer some clues as to the problem.

Best Regards,

Brian Pratt

dgmccaskill responded:  2019-08-12

SeeMS viewer (64 bit 3.0.10051.0) seems to open the file without issue, and recognizes the 4 SIM ions that I defined in the method. If I convert to mzML with msconvert and try opening it with Skyline, I get the same error message as before.

If I can get this to work, it would potentially involve a lot of files, so I'd rather have native support within Skyline (either for the Chemstation files, or for the automatically generated MassHunter files generated from Chemstation).

Thanks for the follow up

Best regards,


Brendan MacLean responded:  2019-08-12

Hi Dave,
Can you give us your Skyline document (use File > Share - Complete to create a file) and an example file (use a utility like 7-zip or Window Explorer to create a ZIP file from your .d folder)? If these are less than 50 MB, you can just attach them to a response on this thread, or otherwise, you can upload them to:

We will have a look at how hard this would be to support. Thanks.


dsullivan responded:  2019-08-30

Hi Dave et al,

We are using Skyline for similar data and ran into this exact issue recently as well.

Our temporary solution is to turn off the SIM channel on the LCMS when acquiring the data. I don't have a solution currently for previously collected data, but I thought I'd suggest this in case you are still having issues.


dgmccaskill responded:  2019-09-03

Ah, so it seems to be specifically the SIM scan data that Skyline is having trouble dealing with.

If I take a look at a previously generated Chemstation file with full scan data which had been converted to MassHunter format using Agilent's script, then Skyline imports the target masses from the full scan MS data without issue.

For me, this solves my problem.