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Messages - QizhiSu

92
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,
Sukis
93
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?
94
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
95
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
97
MS-DIAL / MS-DIAL crash when openning corrDec spectra
Hi Hiroshi Tsugawa,
it is a little bit weird that MS-DIAL crashes when I try to show CorrDec spectra. it only works when I open the defaual spot, and when I open it for other spots, it crashes.

by the way, MS2Dec and CorrDec are two different deconvolution algorithms. so our MS spectra can only be deconvoluted by one of them but not the combination? and we have to check CorrDec one by one?

all the best.

98
MS-DIAL / Re: Post-identification issues
Hi Sergey Girel,
I suppose the problem is not the limitation of the size of the table. I have once encountered a similar problem, and I finally found that one of my entries had a wrong MZ, that was placing whitespace after the decimal point (e.g. 355. 0705 instead of 355.0705). Maybe you can check your list by something like bisection method.

99
MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
Hi Hiroshi Tsugawa,
1. I am sorry that I cannot remember where I have the confusion regarding lockmass in the .raw file. Maybe I have made a mistake, but I am not sure. Anyway, I will keep my eyes on the issue in future use. 
2. As for the problem about importing the library. I found it my fault. The problem was that my library was suffixed with capital "MSP". I now change it into lower cases "msp" and it works fine. It is a little bit odd that my GC-MS library was suffixed with capital "MSP" as well, but it works well.
3. Thank you very much for developing and maintaining the Softwares. They are really excellent and useful.


Best regards,
Sukis
100
MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
Many thanks Matthew. The comment box helps as well. I will refer to the article about correlation-based deconvolution for further detail.

kind of regard,
Sukis
101
MS-DIAL / Few issues about MSDIAL and MSFINDER
Hi,
here are some issues and my own expectations for MSDIAL and MSFINDER.

MS-DIAL (data independent LC-MS/MS)
   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. 
   b. There is always an error "library information should be imported". But I have MSP library downloaded from RIKEN, and use it for the identification. Is it only available when the spot hit any library?
   c. I am wondering if MSDIAL allows manually identification of any feature since the requisite of uploading spectra to MoNA is that the feature has to be fully identified. If I wanna submit the spectrum of a compound, I know which spot is the compound, but how can I assign metadata to that spot and then submit it? And I think it will be useful to allow to export the identified spot as local database, e.g. *MSP file.
   d. Can anybody tell me what is  correlation based deconvolution? I could not find useful information to fully understand what is it for.

MSFINDER
   a.Is it possible to the selected rather than all local databases for formula scoring? I think it will be nice for research areas other than metabolomics.
   b. Is it possible to allow us to mark down the probable correct structure we think? It seems like the "reflect MS-FINDER result to MSP/MAT file" function. The difference is that it would be better to permit us to select the one we want instead of to choose always the top 1 candidate. And it would be very nice to allow exporting the "identified" compound (meta data) together with MS/MS spectrum as a MSP file. It will facilitate building library and then submit to open library since metadata are already there.
Using predicted retention time to structure elucidation is really a good idea. However, is it possible to allow user to integrate their well train model (for example trained and tested by Retip R package) for the prediction instead of using the simple XLogP method?
       

103
MS-DIAL / Retention time prediction doesn't work on the latest version MSFinder
Dear Hiroshi Tsugawa,
I found that retention time prediction in the latest MSFinder (3.42). When I input the *.txt file following the manual, and load it, all compounds get XLogP value of -1, and same predicted RT. However, it works fine in MSFinder 3.30.


best regards,
Qizhi Su
 
105
MS-DIAL / Re: MSFINDER problems
Hi,
Many thanks for your answer.
1. I have downloaded the latest version, only selected local databases were for structures search, but the "resources" still contains databases not selected. Is it designed for purposes that all embedded databases are used for formula search and scoring regardless of any selection? I am wondering if it is possible to use only selected databases for formula as well as structure scoring. or maybe it is better to offer us the option, because for research field other than metabolomics, the embedded databases are not that related and other user-defined databases are preferred.

2. The latest version still have the crash problem, that is when i select "always use pubchem". version 3.30 works fine.