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Topic: Processing CCS files from Waters Vion ? (Read 649 times) previous topic - next topic

Processing CCS files from Waters Vion ?

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

Re: Processing CCS files from Waters Vion ?

Reply #1
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

Re: Processing CCS files from Waters Vion ?

Reply #2
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
 

Re: Processing CCS files from Waters Vion ?

Reply #3
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.


 

Re: Processing CCS files from Waters Vion ?

Reply #5
Note that last time we tried this Waters confirmed that it only works for data that contains an MSE trace. Only god knows why.
Blog: stanstrup.github.io

Re: Processing CCS files from Waters Vion ?

Reply #6
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

Hi 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.


Note 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

Re: Processing CCS files from Waters Vion ?

Reply #7
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

Re: Processing CCS files from Waters Vion ?

Reply #8
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