How to use chromeleon to process LCMS data from Chemstation

submamrine · Joined: 04 Feb 2010 Posts: 6

I have always been using chromeleon and completely new to chemstation. Is there a way that I can transfer LCMS data gathered by agilent chemstation to chromeleon to process? There is a option in chromeleon's menu called import->import from agilent chemstation. When I click this, the window even can recognizance *.B file. But when I try to follow the instruction it always ends up with a error message saying "Not enough storage is available to complete this operation". Has anyone ever come cross this problem before?

unmgvar · Joined: 13 Apr 2005 Posts: 417

I believe that your request is not possible.
the only MS file that can be read by CM to my knowledge are those of excalibur and that if both softwares are installed on the same PC

submamrine · Joined: 04 Feb 2010 Posts: 6

Ha. That is disappointing, I thought Chromeleon could do that... But, how can I use Chemstation to do the same job that chromeleon can. Such as automatically generating a batch report with areas of certain peaks for all samples in a sequence?

lmh · Joined: 08 Aug 2008 Posts: 454

Yes.

Go to the Data Analysis view in Chemstation, and select Batch - load batch. Associated with every sequence you have run (myname.s) there should be a batch file (myname.b). Open this. You can open it using the method by which it was run, or any other method. Then start batch reprocess to reprocess all the data files using the method you selected. At the bottom of the screen is a bar with batch data in it, and some buttons to the right. One of them allows you to set up details of what you want from your batch processing; the columns you would like in an excel spreadsheet containing all the peak areas. Use Output Batch Report to create the spreadsheet.

Once you've done it a few times, this is all quite straightforward, but there is a lot to set up, and I don't know how well you know Chemstation. The biggest job is actually setting up your method to extract all the required mass signals (EICs) and integrate peaks appropriately.

submamrine · Joined: 04 Feb 2010 Posts: 6

lmh and unmgvar, thanks for that. But when I was trying to follow that there is a error message pop up saying "NV--0101.D not loaded". I was using a different computer to process the data other than the one control the machine. After running one sequence, I copied the whole folder with the same name as the finished sequence from \data directory to my computer. Is that possible that there is some other files need for processing but I haven't copied? I tried several of sequences and they all showed the same error.

lmh · Joined: 08 Aug 2008 Posts: 454

It's difficult to diagnose these things from a distance. It should be possible to copy entire folders and get it to work; I do this routinely. It won't work if you copy a folder from a new version of Chemstation and then try to work on it in a much older version of Chemstation.

To exclude difficulties relating to the version or to locations of files, you could start by seeing if the original copy of Chemstation where the data were collected is able to open the data in batch mode. You could also check that both copies of Chemstation are able to open a data file normally, not in batch mode.

submamrine · Joined: 04 Feb 2010 Posts: 6

It seems that chemstation can't process "wash" when there is a was between my samples. This can be easily excluded when loading a batch. After that, think I met the hardest task you said, lmh. I had played around with the various options in batch report option window, but I still can't get it right. Is there a sample of report option window with settings that give area of each peak at selected retention time?