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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

Re: Few questions about MS-FINDER

Reply #1
Dear Qizhi

1. Does it allow deleting files from the file navigator? I think it will be very nice to have this function.
>> 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.


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.
>>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++.


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?

>> no, MS-DIAL does not use such an annotation information currently.

can we export the .msp file without these descriptions?

>> the answer is the same as I describe for the second question.
Overall, I am rewriting all source codes of msfinder and msdial right now, and everything will be improved within this year.

Hiroshi

 

Re: Few questions about MS-FINDER

Reply #2
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