What should we select the reference from setting Analysis parameter setting? is this the blank file. And what is the reference file for isotope tracking? is this the same blank file?
I have 45 file done by GCMS and when i click on PLS , software needs me to put the Y variables , what are the Y variables? I have another question if i have an internal standard file , what is the type of that file ( options are sample, blank, QC , Standard) no internal standard option what can i do? , 3rd question regarding the alignment excel sheet exported ( i do not have the area of most of the compounds, i have -2, 0, -1 instead ) what is the problem ?thank you
Thank you so much. this video is very helpful and so nicely explained. I just did not understand one thing why you multiply the concentration values with 2 during normalization.
Posting a reply from Hiroshi Tsugawa. Please forget the actual number of 2. Instead, what you have to do is to put the concentration (pmol/mg tissue etc) of standard compound in the cells. In our lab, we use EquiSPLASH. avantilipids.com/product/330731 Then, we put 5 microL of the solution into the lipid extraction solvent, and the solvent usually contains the lipid contents from 10 mg tissue sample. Therefore, if the pmol of PC deuterium compound in 5 microL is X, the value (Y) which should be added in MS-DIAL is: Y = X/10
How did he got the reference database for lipids (in identification section at 15:53 min) ? Is that available online or do we need to make it by ourself ? I am working with yeast lipids, what type of database would be appropriate for me ? Thank you.
**This is the reply from Hiroshi Tsugawa. Hope this helps you!** You do not have to take care about the library. MS-DIAL internally contains such a library information. Please start your project as lipidomics mode. Then, if you click "Select" button of identification tab, you will see the lipid class list, and please select what you want to annotate for your data.
Hii, I am working on lc-ms data, i have 50 files and out of which I have one QC ms/Ms file and rest are full scan data now I wanted to annotate and identify the metabolites. But the problem is, each file have one result and I am getting nothing in those files, only in ms/ms file there are ions present rest are empty.
What should we select the reference from setting Analysis parameter setting? is this the blank file. And what is the reference file for isotope tracking? is this the same blank file?
hi do you know how to export GCMS data in a GNPS mode, as I cannot export GNPS data, it cannot be checked.
I have 45 file done by GCMS and when i click on PLS , software needs me to put the Y variables , what are the Y variables? I have another question if i have an internal standard file , what is the type of that file ( options are sample, blank, QC , Standard) no internal standard option what can i do? , 3rd question regarding the alignment excel sheet exported ( i do not have the area of most of the compounds, i have -2, 0, -1 instead ) what is the problem ?thank you
is your problem solved?
Thank you so much. this video is very helpful and so nicely explained. I just did not understand one thing why you multiply the concentration values with 2 during normalization.
Posting a reply from Hiroshi Tsugawa.
Please forget the actual number of 2. Instead, what you have to do is to put the concentration (pmol/mg tissue etc) of standard compound in the cells.
In our lab, we use EquiSPLASH.
avantilipids.com/product/330731
Then, we put 5 microL of the solution into the lipid extraction solvent, and the solvent usually contains the lipid contents from 10 mg tissue sample.
Therefore, if the pmol of PC deuterium compound in 5 microL is X, the value (Y) which should be added in MS-DIAL is:
Y = X/10
@@lipid-maps Thank you for your reply it was helpful.
How did he got the reference database for lipids (in identification section at 15:53 min) ? Is that available online or do we need to make it by ourself ? I am working with yeast lipids, what type of database would be appropriate for me ? Thank you.
**This is the reply from Hiroshi Tsugawa. Hope this helps you!**
You do not have to take care about the library. MS-DIAL internally contains such a library information.
Please start your project as lipidomics mode.
Then, if you click "Select" button of identification tab, you will see the lipid class list, and please select what you want to annotate for your data.
Hii, I am working on lc-ms data, i have 50 files and out of which I have one QC ms/Ms file and rest are full scan data now I wanted to annotate and identify the metabolites. But the problem is, each file have one result and I am getting nothing in those files, only in ms/ms file there are ions present rest are empty.