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Topics - QizhiSu

16
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.
17
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
18
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
19
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
20
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