mass error (ppm) for peptides

mass error (ppm) for peptides kmsd  2024-01-19 12:42

I am trying to find the mass error for BSA QC sample to compare the replicates from day to day run. I know mass error for small molecules are available in skyline but when I tried to do it for peptides using TSQ Altis plus it was not showing up in skyline. I am using

Nick Shulman responded:  2024-01-19 12:51
Skyline only calculates mass error on high-resolution full scan instruments.

It would be impossible to determine mass error on a triple quad instrument such as the TSQ Altis because the signal that the instrument measures does not have any information about where the observed mass is within the isolation window.

In order to see mass errors in Skyline, the chromatograms need to have been extracted from spectra. Also, the mass analyzer at "Settings > Transition Settings > Full Scan" cannot be "QIT" because QIT is low resolution.

-- Nick