Isobaric labeling in small molecules

Isobaric labeling in small molecules Juho  2019-04-16

Dear all,

I would like to go trough results of isobarically labeled small molecules (TMT/iTRAQ etc) that were combined for smaller number of samples and measured using scheduled PRM. Now the individual reporter ions present individual samples or standards with different concentrations and I would like to set the analyte concentration based on product m/z and replicate. For the quantification I try to set concentrations from the document grid individually, but skyline prefills all same analyte concentrations of the same replicate and same precursor regardless of different product m/z.

Is there a way to fill individual product m/z of the same precursor m/z and same replicate with different concentration for quantification with Skyline or should I just export integrated peaks and do this in a spreadsheet?

Many thanks,

Brian Pratt responded:  2019-04-16

Hi Juho,

I don't think that's something Skyline is set up to handle. We think of concentration as a replicate property, as you've seen. You'll have to pursue that analysis by some other means, like a spreadsheet as you say.

Best Regards,

Brian Pratt

Juho responded:  2019-04-16

Thank you Brian for the fast reply!