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Messages - liyong189108

3
MS-DIAL / About the retention time in the msp library.
Hi Hiroshi,
I am curious about the retention time records in the msp library(eg. the All public MS/MS (13,303 unique compounds)). Were these records produced under the same LC codition? If yes, what is the condition?

Best wishes!
Yong Li
4
MS-DIAL / About the identification result.
Hi All,
 I found something wierd about the identification result of  my LC-MS/MS profiling data,  The identification score cut off was set as 90% (see the attached screen shot) and a list of metabolites were identified. However, the annotation  seems  performed only based on MS1 ions. All identified metabolites in the exported alignment result table were annotated as false "MS/MS matched"  while the  total  scores were mostly more than 90 (see attached table). I have checked some of the annoted candidates and  make sure that the MS2 spectral was not matched well with  the reference spectral. I can't understand the scoring rules because I think the candidate MS/MS spectral should matched very well with the library spectral when  a high score was given. Could you please help me to remove this confusion?

Thanks

Yong Li
6
MS-DIAL / About the molecular spectrum networking
Dear developer,
Thank you very much for the amazing software, the MS-dial. I just found something can be improved about the exported edge file of the molecular spectrum networking with the 'export ion abundance correlation among samples' was selected. There were two kinds of networkings existed when I performed the spectrum networking coupled with the abundance correlation. However, both of the two  networkings were classed as 'spectrum similarity ' in the txt edge file. It is hard to distinguish these two networkings when I import this  file to Cytoscape for further visulization. Waiting for your response!

Best wishes!
Yong Li
7
MS-DIAL / Re: question about QuantMass
Option-->alignment result property setting, then you can input what you like!
In my opinion, QuantMass does not necessarily be the major mass. I think the most abundant unique mass is the ideal QuantMass.
8
MS-DIAL / About mass calibration of data produced by Qtof MS
Hi Hiroshi,
I am going to use the MS-DIAL to process metabolomics raw data produced by uplc-qTOFms (Bruker Impact II). Calibration solution (Sodium formate) is used for mass calibration in my experiment. Basically, the calibration solution elutes at the dead time of the RP chromatography and the metabolites follow. However, I do not know how to do mass calibration using the MS-DIAL and I can not find the instruction about it. Should I calibrate the raw data before I input it to the MS-DIAL?


Best wishes!

Yong Li
10
MS-DIAL / About the use of MS-DIAL
Hi guys,
I have some questions about the use of MS-DIAL. The first question is I can not find a place to assign the internal standard when I run the latest version 4.12. The instruction say it do has a place to assign the IS. But the Instruction was written based on the version 2.28. Since the MS-DIAL has more than fifty versions, does it have a instruction about the difference of these versions?
The second question is about the result of identification.  Is the software has an access to modify the identification result?
The third question is about the result of alignment. We want to use the MS-DIAL for pathway mapping and correlation analysis of data from different platforms. But we do not know how to merge the alignment results from different platforms and use it for MS-DIAL based pathway mapping and correlation analysis.
Could you please help me?