Report file

Report file zainab noor  2018-11-15

Dear Skyline team,

I have to export the report file from skyline with the peptide and peptide intensity column. Which column should I use to extract the total intensity of each peptide in each replicate? Is it Max Height under Precursor Results?

Kind regards.

Nick Shulman responded:  2018-11-15
The column that you should use is "Normalized Area".
It's under:
Proteins > Peptides > Peptide Results > Quantification

The Normalized Area is the are for the peptide, normalized according to whatever you may have specified at:
Settings > Peptide Settings > Quantification > Normalization Method

If you haven't specified a normalization method there, then the Normalized Area of a peptide is just the sum of the areas of all of its individual transitions across all of its precursors.
zainab noor responded:  2019-02-05
Hi Nick,

I have exported the peptide intensities and I want to see the protein intensities. Is it simply the sum of intensities/areas of all of the protein's individual peptides? Can I export them directly from Skyline report form, if yes, which column should I use?

Thanks in advance.