Metabolomics Society Forum

Dear all,
Does anyone know how to convert a ".row" file data from waters instrument which contains "ion mobility data"  into a format that I can process just ion mobility files on XCMS.

Thanks for help!


--Fereshte

Fereshte,

I would expect that the DataBridge should be able to convert the files. I have not had the chance to play much yet with the ion mobility data yet. Let me know how you get on.

Paul

Paul,
Unfortunately,  DataBridge can not convert ion mobility data however I tried it. After conversion, the "NetCDF "file didn't contain ion mobility data. :(

Fereshte,

Normally with DataBridge each part of the mass spect data is split into different files. For example if we have MS data and UV detector data then the UV detector data is placed into a separate file. Do you have more than one CDF file that is made?

Otherwise I'm not sure. I would have a play with the 'msconvert' but I wouldn't expect much.
http://proteowizard.sourceforge.net/downloads.shtml (http://proteowizard.sourceforge.net/downloads.shtml)

Paul

Fereshte,

Are you using LC/some other separation, or just doing direct infusion?

If you're just doing direct infusion of samples, then you can export IMS data from Driftscope with the retention time data stripped, then treat it just like LC/MS data (with very short retentin times). I'm just learning this stuff, but I've been using MSConvert to get into mzXML files, then the world is your oyster. Oh, if you export with the drift time in ms, you need to divide by 60 (along with some factor of 10 I can't remember off the top of my head) to get the drift time in ms.

If you're using a separation, I'll be waiting here to see how you go about it....

Good luck,

ajsp

ps. Are there many other people dealing with IMS-MS data here?

Hi ajsp, I am using LC in combination with Mass Spec (Ion mobility mass spec). I am still looking for a method/technique/software to convert my ".raw " data file to a file which contains only ion mobility data (drift time)!  Actually, I can export my data manually one by one, but with large number of samples, it is a totally time consuming approach!!!
 
Please let me know if you could figure out a way to resolve this problem.

Thanks,Fereshte

Fereshte,

I haven't got my head round this yet, I'm afraid. I have been in contact with the Waters application people, but they weren't able to help much beyond what I've already worked out (in fact they weren't even able to point me as far as I have arrived). I imagine that it must be possible or being developed at the moment, as they are selling more and more of these machines......

When you say that you want to convert you .raw to something with ONLY ion mobility data, do you mean only DT data (as opposed to DT vs. RT, or DT vs. m/z)?

Andy

Hi Andy,
I want to have "mass to charge ratio" vs. "DT"  :)
I have also contacted with waters people so many times, and they couldn't help me with this!!!!!!! So wired that they even don't know the solution for my problem!!!!!

Fereshte

Fereshte (or anyone else hanging around),

Still no useful advance on the approach I outlined before, but you may be interested in checking out a program called "Amphitrite" from the Thalassinos group in London. It doesn't seem to be available online yet, but "soon", and there is a publication describing it here: http://http://dx.doi.org/10.1016/j.ijms.2012.09.005

It looks rather handy - I'm certainly keen to dump my bespoke procedures and use it for some things when I can get my hands on it.

Andy

Has anyone used masswolf to convert HD-MSE to mzXML. I have converted files but I am not really sure if the ion mobility data is retained.