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Messages - Sukis

MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
Hi Hiroshi,

" a. When dealing with Waters MSE data, in my experience, it is better to remove function 3 files (_FUNC003.DAT, _FUNC003.IDX, AND _FUNC003.STS, they are for the lockmass) from the *.raw file before converting into *.abf file for MSIDAL processing. Otherwise, the deconvoluted MS/MS spectra might weird.

According to my understanding, the function storing lock mass data is not stored in abf. If you see such an issue, we have to ask the developers of abf converter. Please send me an example .raw file of Waters if you face on such an issue."

I recently encountered this problem again. i think i find a good example now.

I upload two screenshots here. after removing the function 3 from the raw file, the deconvoluted MS/MS is much better.

maybe I can send you my file when you have time.

MS-DIAL / Some GC-MS peaks donot correctly aligned

I found that some GC-MS peaks do not align correctly. For example, benzaldehyde and 1.2.4-trimethylbenzene have quite difference spectra according to the NIST library, however they are aligned as one peak and only 1.2.4-trimethylbenzene is reported even though I have set 80% spectrum similarity for the alignment (please see the attachment). Does anybody know what is wrong here?

thanks in advance.
MS-DIAL / Re: Processing CCS files from Waters Vion ?
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:

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.

MS-DIAL / Re: Processing CCS files from Waters Vion ?
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.
MS-DIAL / Re: Processing CCS files from Waters Vion ?
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.

Qizhi Su
MS-DIAL / Re: Few questions about MS-FINDER
Dear Hiroshi,
Thanks a lot.
1. The file navigator just recognizes the existence of msp/mat files in the imported directory. Therefore, if you transfer them into a different directory, the files are not existed anymore in the file navigator. Therefore, sorry, I think there is no smart way to delete files in the file navigator of MS-FINDER program
   >>>> Yes, I notice now that I can delete peaks that I don't want from the folder.

2. Currently, of course no option to do that. (but I think, you do not have to use MS-FINDER if the annotation is not needed, right...?) Simply, it's a bit tedious for an end users, the annotation can be deleted by a regular expression in e.g. notepad++
  >>>>>In this case, I use MS-FINDER for exporting *.MSP file of known standards. it is fine to delete them by a regular expression.

3. Overall, I am rewriting all source codes of msfinder and msdial right now, and everything will be improved within this year
>>>> thanks a lot for your great effort!

all the best,
Qizhi Su
MS-DIAL / Which data formats are supported by IBFconverter?
Hi everyone,
I obtained ion mobility data from Waters Vion instrument, but all data is managed by .uep format. I can now export data by MSconvert. But .XML file is not supported by IBFconverter. Does anybody know which data formats are supported by IBFconverter?

all the best,
MS-DIAL / Re: IBF convertor from command line
I am sorry that I couldn't help you for the command line. but i would like to know more detail. could you please tell me which instrument did you use and what is the data format you have for IBFconverter?
MS-DIAL / Few questions about MS-FINDER
Dear Hiroshi Tsugawa,
I have a few questions about using MS-FINDER, could you please help?
1. Does it allow deleting files from the file navigator? I think it will be very nice to have this function.
2. Does it allow exporting results as .MSP file without peak annotation?  I understand that the peak annotation is helpful to get cleaner spectra when building a library. But sometimes the spectrum seems to be overcleaned that the cleaned spectrum is not representative.
3. when exporting .MSP file from MS-LIMA, the obtained .MSP file has descriptions about each peak that is annotated by MS-FINDER. I have tried that, this .msp file can be used for MS-DIAL, but I am just thinking this information seems not necessary for a library no? can we export the .msp file without these descriptions?

all the best,
Qizhi Su
MS-DIAL / 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