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Messages - QizhiSu

106
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.
107
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.
108
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
109
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.
110
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
112
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
115
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
116
MS-DIAL / Re: How does MS-DIAL take representative spectra?
Yes, I can find good spectrum in the sample that has highest peak, but no good match in near retention time area. But sorry, I don't understand what do you mean "define the quant mass field that does not share co-eluting metabolites each other"? I am thinking if it is possible to keep only the alignment spot that has the highest match when there are many spots in similar retention time and same quan mass.

By the way, I would like to know 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 that that in blanks, but not 0.  Will those samples be included in the "fill"? can we set that if a sample have S/N ratio lower than a certain value, they will not be regarded as positive samples, and their S/N or height can be set as null. In this way, we can know easily know which sample is truely positive/negative.
118
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