PRM relative label free quant

adrien schmid

2018-12-07 00:30

Dear Skyline team,

I would like to inquire if the scientific community uses a combined PRM approach, where some targeted peptides are monitored along their heavy labelled surrogate peptides for absolute quantification (standard PRM approach), whereas within the same PRM method, a sub population of peptides (of different proteins) are only targeted for monitoring any changes in relative abundance between biological samples? This would resemble a label free (relative) quantification method using MS2 spectra for assessing the changes in relative abundance of a protein.

Would this make sense ?
many thanks for your feedback on this question.
best regards

Adrien

Nick Shulman responded:	2018-12-10 12:21
I do not know whether scientists actually do this, but Skyline does allow you to have different normalization methods for different peptides within the same Skyline document. If you want to compare abundances between different groups of replicates, you should take a look at the group comparison tutorial: https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped When you are setting up a group comparison in Skyline, you can specify the normalization method on the "Edit Group Comparison" dialog. If you have some other peptides that you want to use a different normalization method, you can use the Document Grid to change the "Normalization Method" values. The "Normalization Method" column is part of the "Peptide Quantification" view. If you want to do absolute quantification with calibration curves made from external standards you should take a look at the Absolute Quantification tutorial: https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_absolute_quant If you want to learn about the Document Grid, you can take a look at the Custom Reports tutorial: https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports -- Nick