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Topics - Sukis

1
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.
2
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
3
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
4
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
5
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.

6
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
 
8
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
9
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.
10
MS-DIAL / How MS-DIAL calculates the "fill"
Hello, Hiroshi,

Could you please explain to me how MS-DIAL calculates the "fill"? because I found that in many cases, the S/N ratio of a certain alignment spot in many samples is small than that in blanks, but not 0.  Will those samples be included in the "fill"? I am guessing that MS-DIAL calculates S/N or height/area of each spot once it detects the quan mass. but it seems more reasonable to calculate those values only when the spectrum correspondent to that spot, let's say when spectrum similarity higher than 80%. by this way, we can know which samples really contain that component. because when i checked my data, i found that some samples have very high S/N ratio of a certain spot, but actually the component is absent in those samples.

In addition, it will be of great help to have a single column tell that which samples have that component.

best regards,
Sukis
11
MS-DIAL / Transform NIST library into *.MSP file together with retention information
Hi everyone,

Does anybody know how to convert NIST library into *.MSP file together with retention index information? it will be of great help to use that *.MSP library for GC-MS features annotation in MS-DIAL. I have tried to use lib2nist for this purpose, however, there is no retention index when applying MS-DIAL. I am not sure if the problem is the *.MSP file or MS-DIAL cannot recognize it. We have a library named W10N14, I am not sure what is it, but I guess it is a combination of Wiley and NIST library. When I convert this library into *.MSP file, MS-DIAL can recognize retention index information. The problem is that W10N14.MSP uses both real and estimated retention index. for high accuracy annotation, I think using the specified retention index (selected column type) like NIST MS search does is good. However, how to prepare a library with retention index information (specified column type) is a problem. I am thinking if it is possible to modify the *.MSP file by retrieving the specified column type retention index from NIST website, but unfortunately, I am know how to program.

any suggestion will be appreciated!

Thanks a lot.

best regards,
Sukis
12
MS-DIAL / How does MS-DIAL take representative spectra?
Hello everyone,
Can anybody explain to me how does MS-DIAL take a representative spectrum for each aligned peaks? In my GC-MS project, I recently found that there are many peaks that remain unidentified possibly due to the representative spectra were not good. I say that because when I manually checked their spectra in AMDIS, many of them can be identified with a high match. I was thinking if the problem was the deconvolution process; however,  I have tried to use different sigma values (0.3, 0.5, and 0.7) for deconvolution and it did not improve too much. In addition, many of them have a unit peak in the chromatogram. As such, I prefer to know how does MS-DIAL takes the representative spectrum. Maybe I have too much samples for alignment, and MS-DIAL did not take the best spectrum for some peaks?

Thanks in advance.

best regards,
Qizhi Su
13
MS-DIAL / Export alignment results to .MSP file with retention time, S/N, etc. information
Dear Hiroshi and MS-DIAL developers,

Thank you very much for your great effort in developing and maintaining MS-DIAL. I am thinking if it is possible to export alignment results (representative spectra) to MSP files together with metadata, e.g. retention time, S/N, etc. MS-DIAL has a very good option to search against MS libraries though, it is a little bit tricky when searching against NIST as well as Wiley libraries because they don't have RI information suitable for MS-DIAL. After identified by MS-DIAL, I still have to check each identification using RI information. For me, it is more convenient to use the NIST MS Search. However,  the .MSP file exported from MS-DIAL does not contain metadata, retention time, S/N, etc., and it is a little bit tricky to correspond MSP entry to the peak spot. Is it possible to incorporate metadata, especially retention time, when exporting the alignment results (representative spectra) into .MSP file?

Kind regards,
Qizhi Su