Ion Mobility data January 31, 2013, 08:03:01 PM 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 Quote Selected
Re: Ion Mobility data Reply #1 – February 02, 2013, 11:44:10 AM 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 Quote Selected
Re: Ion Mobility data Reply #2 – February 05, 2013, 05:19:06 PM Paul,Unfortunately, DataBridge can not convert ion mobility data however I tried it. After conversion, the "NetCDF "file didn't contain ion mobility data. Quote Selected
Re: Ion Mobility data Reply #3 – February 05, 2013, 11:59:21 PM 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.shtmlPaul Quote Selected
Re: Ion Mobility data Reply #4 – February 18, 2013, 04:45:25 PM 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 Quote Selected
Re: Ion Mobility data Reply #5 – February 18, 2013, 04:55:35 PM ps. Are there many other people dealing with IMS-MS data here? Quote Selected
Re: Ion Mobility data Reply #6 – February 24, 2013, 09:09:09 PM 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,FereshteQuote from: "ajsp"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 Quote Selected
Re: Ion Mobility data Reply #7 – March 04, 2013, 05:43:02 AM 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 Quote Selected
Re: Ion Mobility data Reply #8 – March 05, 2013, 04:39:16 PM 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 Quote Selected
Re: Ion Mobility data Reply #9 – July 04, 2013, 04:13:12 AM 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.2012.09.005It 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 Quote Selected
Re: Ion Mobility data Reply #10 – August 26, 2013, 09:01:14 AM 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. Quote Selected
Topic: Ion Mobility data