Discrepancy in Skyline and Mass Lynx M/Z values

Discrepancy in Skyline and Mass Lynx M/Z values sa825  2021-10-06


I wanted to ask why Skyline and Mass Lynx are showing different M/Z values for the same peptide.

It's a peptide with the sequence: ADCLTQCAAR. In skyline, the heavy peptide comes up as 588.2622 but in Mass Lynx, its 588.3.
Is there a way to change the M/Z value in Skyline to match the one in Mass Lynx? As I have the results form Mass Lynx using the M/Z 588.3 and when I bring those results into skyline, the chromatograms are empty.

I have attached some screen shots to explain. The M/Z in question is the one tagged "BCR5 ISltd" in the Mass Lynx screenshot.


Nick Shulman responded:  2021-10-06
It looks like MassLynx is rounding those m/z values off to one decimal place.

There are a couple of different settings which control how closely numbers in other tools have to match what Skyline calculated.

One setting is "Method match tolerance m/z" at "Settings > Transition Settings > Instrument". This setting is used during chromatogram extraction to decide whether a particular MS2 spectrum matches a precursor in your document. This setting is also used when deciding whether the Q1 and Q3 values of a SRM chromatogram match a precursor and transition in the document.

The other setting is "Ion Match Tolerance" at "Settings > Transition Settings > Library". This setting is used to determine whether a peak that is seen in a library spectrum matches a particular transition.

I am not sure which of those two settings will fix the problem you are having with MassLynx, but I think if you change both of those settings to 0.55 it might work.
-- Nick
sa825 responded:  2021-10-06
That worked, thank you so much!