Processing CCS files from Waters Vion ? June 10, 2020, 01:16:04 AM Hello everyone, MS-DIAL now is capable to process ccs profile. Does anyone have experiences to work with Waters Vion ccs file (UNIFI)? how can I export data from UNIFI and then process them in MS-DIAL?best regards, Qizhi Su Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #1 – July 12, 2020, 07:42:02 AM Hi Qizhi,sorry, the past one month was crazy for me. About UNIFI, I personally do not have an experience for parsing the data. Is there a demo file to check the format on my side? Also, as a practical thing, you can convert it into ibf via mzML if the unifi data can be converted to the mzML format.Thanks,Hiroshi Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #2 – July 14, 2020, 04:17:35 AM Dear Hiroshi, Our UNIFI is capable to export *.mzML and *.mzXML using MSconverter. I have tried *.mzXML before, but it didn't work. I will try *.mzML and let you know how it will be going. regards,Qizhi Su Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #3 – July 14, 2020, 06:03:40 AM Unfortunately, MSconvert does not support to convert raw files from UNIFI as I attached. it specifies that it does not support UNIFI when applying peak picking filter. Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #4 – July 16, 2020, 04:35:24 AM To export from UNIFI you must open a port on the server and connect MSConvert to it via network. For this you have this "Browse network resource" field in the upper part of the window.Here is Waters guide for it: https://support.waters.com/KB_Inf/UNIFI/WKB78812_How_to_set_up_MSConvert_with_the_UNIFI_Web_API Quote Selected 1 Likes
Re: Processing CCS files from Waters Vion ? Reply #5 – July 16, 2020, 06:31:33 AM Note that last time we tried this Waters confirmed that it only works for data that contains an MSE trace. Only god knows why. Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #6 – July 17, 2020, 01:54:20 AM Quote from: Sergey Girel – on July 16, 2020, 04:35:24 AMTo export from UNIFI you must open a port on the server and connect MSConvert to it via network. For this you have this "Browse network resource" field in the upper part of the window.Here is Waters guide for it: https://support.waters.com/KB_Inf/UNIFI/WKB78812_How_to_set_up_MSConvert_with_the_UNIFI_Web_APIHi Jan Stanstrup, thanks a lot for your help. I know how to connect MSconvert and UNIFI. The problem is which filter should I use? As peak picking filter using vendor format does not support UNIFI. I have tried to use peak picking applying CWT setting. it can be converted to*.ibf file and processed by MS-DIAL. The accuracy of the mass, retention time as well as drift time are perfect, but the deconvoluted MS2 spectra seem weird. I attach the spectra of a standard from UNIFI and MSDIAL below to show the difference. it seems something wrong with the MS-DIAL MS2 deconvolution. As MS-DIAL works perfectly for MSe data, i suppose the problem could be the converted *.mzML file. by the way, does anybody know how go get the coefficient for calculating Waters ccs values? As the ccs values obtained in MS-DIAL were far from correct. I suppose it is because I didn't set these values when processing with MS-DIAL.Quote from: Jan Stanstrup – on July 16, 2020, 06:31:33 AMNote that last time we tried this Waters confirmed that it only works for data that contains an MSE trace. Only god knows why.we work with MSe data, so it is okay for us.regards Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #7 – August 13, 2020, 10:58:46 PM Hi Sukis,for usual Waters data processing, MS-DIAL will parse mob_cal.csv file for retrieving CCS calibration data. However, when converting the unifi data into mzml, the calibration information is not existed, right?If the mzML file does not include the information, currently, there is no way to calculate CCS values in the MS-DIAL program. Could you please share one UNIFI data with me? I can ask the Waters developer's team to deal with the data on my side.Thanks,Hiroshi Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #8 – August 14, 2020, 12:05:00 PM Hi Hiroshi, I don't think there is mod_cal.csv file in the converted mzML file. I will send you both the converted mzML file and the raw .*uep file from UNIFI. regards, Sukis Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #9 – November 25, 2020, 05:16:56 AM Dear Hiroshi,Do you have a solution to work with Waters Vion ccs file (UNIFI) now? or Could you tell me which equipment did you use for testing MS-DIAL? It could be useful information when considering to buy a new equipment.Best,Sukis Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #10 – December 24, 2020, 09:33:21 AM Hi Sukis,sorry for this very late reply. Recently, Dr. Kyo Bin Kang successfully uses MS-DIAL for UNIFI data but not for IM-MS.What he did is to generate ".raw" format file by the UNIFI system, then, he used abf converter. That's all actually. If the ibf converter does not work for the .raw file format generated by the UNIFI system, please let us know. I am very sorry for this inconvenience.Thanks,Hiroshi Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #11 – December 27, 2020, 03:50:16 PM Hi Hiroshi, Never mind! I will try as you suggested. Anyway, I am very grateful for your effort.best,Sukis Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #12 – January 04, 2021, 09:51:53 AM Quote from: Hiroshi Tsugawa – on December 24, 2020, 09:33:21 AMHi Sukis,sorry for this very late reply. Recently, Dr. Kyo Bin Kang successfully uses MS-DIAL for UNIFI data but not for IM-MS.What he did is to generate ".raw" format file by the UNIFI system, then, he used abf converter. That's all actually. If the ibf converter does not work for the .raw file format generated by the UNIFI system, please let us know. I am very sorry for this inconvenience.Thanks,HiroshiHi Hiroshi, Could you please tell me how to export .raw file from UNIFI? because our Waters technician told me that it is not possible to export .raw file. I am confused. Or maybe you can give me the emial of Dr. Kyo Bin Kang, so that I can contact him directly. Best,Sukis Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #13 – January 04, 2021, 11:51:48 PM Hi Sukis,I will directly email to you.Hiroshi Quote Selected
Re: Processing CCS files from Waters Vion ? Reply #14 – March 10, 2021, 11:49:11 PM Hi Sukis,if possible, could you please write the way for UNIFI data handling here if succeeded? (I was asked by a researcher who wanna process UNIFI data by MS-DIAL. Thanks,Hiroshi Quote Selected