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Messages - Sukis

1
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.

2
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.

3
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
4
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
5
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?
       

7
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
 
9
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.
10
MS-DIAL / Re: MSFINDER problems
Thanks for your answer. I have tried many times. It seems to happen only when I check "only use when there is no query in local DBs" or "always use it" in the pubchem online setting.
11
MS-DIAL / Re: MSFINDER problems
I now find out that only when I check "only use when there is no query in local DBs" or "always use it" in the pubchem online setting.
12
MS-DIAL / MSFINDER problems
Hi everyone,

I am not sure if it is suitable to report MSFINDER problem here, but I do not find MSFINDER specific forum.
1. the latest version MSFINDER 3.40 crashes in my computer (win 10 64 bit), but version 3.32 works fine.
2. in MSFINDER 3.32, even though I uncheck many local databases, the final result still take them into account. for example, I only want to use my own database but not any of those embedded database. does anybody know what is wrong?

best regards
13
MS-DIAL / Improving the speed of opening Compound Search for GC-MS data
Dear MS-DIAL developer,

I am thinking if it is possible to improve the speed of opening Compound Search window when dealing with GC-MS data. I am currently using NIST library. I found that it is very slow to open the Compound Search window (ca. 1). I am wondering if the problem is that Compound Search lists all entries in the library. however, most of them are not useful and might slow down the opening speed. as such, i am asking if it is possible to limit the number of entries in the Compound Search list, for example, 100 entries by default. Or, it would be great to offer users an option to choose how many entries do they want to display.

best regards.
14
MS-DIAL / Re: How MS-DIAL calculates the "fill"
Hi Hiroshi,
I understand what you mean, but it is tricky to check which samples really contain a certain metabolite manually no? I am just thinking if it is possible to include this information in the export files? that would be great.

Thank you very much.

kind regards,
Sukis