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Messages - QizhiSu

78
MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
Hi Hiroshi,

Thanks a lot for testing. I understand now it was because of the abf converter I used (an old version probably). Downloading the latest abf converter, it works fine now.

regards.
79
MS-DIAL / Re: Processing CCS files from Waters Vion ?
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
82
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.


85
MS-DIAL / Some GC-MS peaks donot correctly aligned
Hello,

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.
87
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: 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
88
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.
89
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.

regards,
Qizhi Su
 
90
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