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internal Standard

Dear developers,
I would like to better understand how and where to set the information of the internal calibrants to make the normalization of chromatographic runs.
I would also like to understand what they are and how to use the parameters that show ion table and specifically Fill and Correlation
Thanks for your work, you have created a software which is the MaxQuant of Metabolomics! 8)
all the best

Re: internal Standard

Reply #1
Hi,

sorry for this late reply. I was actually very sick last week...
>>I would like to better understand how and where to set the information of the internal calibrants to make the normalization of chromatographic runs.

Sorry, I will remake the tutorial on my website soon, but currently, the "IS ID" column name was changed to "Target ID". So,
1. Go to Option->Alignment result property setting
2. Then, you will find the attached window.
3. Check the alignment spot ID of your internal standard. (If the alignment id of IS is 100,) Please add 100 on the cell of Target ID.
4. Right click on the Target ID column area-> Auto fill -> Then, all cells will be filled by 100.
*You can easily set one internal standard like this, but if you have multi-ISs and if you wanna apply them to the independent peaks, you can do the similar things although it's a bit tough task...
5. Go to "Data visualization" -> Normalization -> Internal standard-> Done
6. Then, all your data will be normalized.
7. The normalized data can be exported from Export -> Alignment result export -> check "Normalized".

>> would also like to understand what they are and how to use the parameters that show ion table and specifically Fill and Correlation

"Fill"
see: http://www.metabolomics-forum.com/index.php?topic=1403.0

"Correlation"
see: http://www.metabolomics-forum.com/index.php?topic=1385.0
Correlation is very simple function where the correlation of ion abundances among samples are calculated between aligned spots, then, you can check the aligned spots having similar metabolic profiles there.

Thanks,

Hiroshi


Re: internal Standard

Reply #2
this time it was my turn to be sick!
thank you very much for your kind and complete reply.
I also take this opportunity to ask for clarification on "correlation-based deconvolution" and the 4 possibilities "Setting and run", "Identification",  "Run single spot" and "Show CorrDec Spectra". I would like to understand when they should be used and with what attention.
thanks again for your wonderful work.

Re: internal Standard

Reply #3
Hi,

I am the main developer of "correlation-based deconvolution" (CorrDec).
CorrDec requires more than 6 samples (>30 is better) to calculate correlation among samples.

- Setting and run
This is the main function, CorrDec will run for all alignment spots.

- Identification
The identification process will start using the CorrDec spectra.

- Run single spot
This is a quick function as a test. CorrDec will run for a selected alignment spot.

- Show CorrDec spectra
CorrDec spectra window will be launched to check the results.

Best,
Ipputa