Modified Sequence Full Names - apparent bug

Modified Sequence Full Names - apparent bug Nathan Manes  2019-04-29

There is an apparent bug in the current version of Skyline 64bit (v4.2.0.19072). When exporting a report that includes precursor "Modified Sequence Full Names", sometimes a mod will be missing. Out of 321 peptides that I imported (Edit --> Insert --> Peptides) into a new document, two had this error (in both, cys carbam was missing in the heavy form; strangely it is present in the light form). Inside the attached ZIP (Modified Sequence Full Names - apparent is the Skyline file with the 2 peptides and the resulting exported report (transition list) with the incorrect "Modified Sequence Full Names" values (heavy rows are incorrect; light rows are correct). I didn't check if anything else is incorrect.

Nick Shulman responded:  2019-05-03
Thanks for reporting this bug.
This bug happens if you have explicit modifications on your heavy precursor. In that case, the implicit modifications (i.e. "C[+57]") are not getting included in the Modified Sequence in the document grid.
I will try to figure out the best way to fix this, and the fix will appear in an upcoming release of Skyline-Daily.
-- Nick