600 is not being accepted in skyline to build spectral library malikshagufa93  2023-05-18 03:18
Hi, I am new to Skyline and trying to build a spectral library using a mouse peptide atlas,the precursor and fragmented ions value is 50ppm/600ppm, and its not being accepted in the software saying ppm value should be below 100. But in the paper, the values are clearly mentioned in the same way.
Nick Shulman responded:  2023-05-18 07:59
If the tolerance is more than 100ppm, then Skyline requires you to express it in terms of Daltons instead of ppm.

The "Adjust Search Settings" page of the Import Peptide Search wizard asks you for the MS1 and MS2 tolerances.
For each of these settings there is a textbox where you can enter a number and dropdown where you can choose either "ppm" or "Da" for the unit.
If you wanted to enter 600ppm, I would probably recommend that you enter "0.6" in the text box and choose "Da" in the Unit dropdown.
600ppm and 0.6Da are the same when the ion's m/z is 1000, but, of course, 0.6Da is a fixed amount whereas 600ppm would be a different amount depending on the m/z of the ion.
-- Nick