SKYLINE sensitivity vs Waters MassLynx

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SKYLINE sensitivity vs Waters MassLynx sesharma  2024-10-15 11:23
 

Compound 1 uses the same parameters and at the same concentration shows:
Analyte area in MassLynx: 38511.961
Analyte area in SKYLINE: 2356949

Compound 2 uses the same parameters and at the same concentration shows:
Analyte area in MassLynx: 30827.227
Analyte area in SKYLINE: 1851899

I am experiencing the above discrepancy. Would you suggest any possible explanation as to why the data analysis through SKYLINE is 100 folds more?

 
 
Nick Shulman responded:  2024-10-15 11:40
In general peak areas that you get from Skyline for a single analyte will not be directly comparable to the values that you get from other software, but may be scaled by a constant amount.
That means that while you cannot directly compare values from Skyline and other software, the ratios that Skyline comes up with will be the same as the ratios that you get in other software.

In this case, the Skyline numbers seem to be about 61 times larger than what you are getting in MassLynx.
That is very close to 60, which likely means that Skyline is using units of seconds and MassLynx is using units of minutes.

Hope this helps,
-- Nick
 
Mike MacCoss responded:  2024-10-15 19:20
Here is a paper that compares Skyline vs Water's TargetLynx software. https://pubmed.ncbi.nlm.nih.gov/29203474/
Measured areas will need to be calibrated to be compared between software tools.

Cheers,
Mike