Modifications show same masses when rounded

Modifications show same masses when rounded hassan hijazi  2024-06-12 08:29

Dear Skyline team,

When having two modifications in the same Skyline document, and we choose to see modifications as mass difference, the mass difference will be the same for modifications of masses when rounded to first decimal digit will identical.

Example 1:

Formyl (K) [+27.994915] and Dimethyl (K) [+28.0313] will both appear as [+28] when choosing: View > Modifications > Mass Difference.

Example 2:
The same applies to trimethyl (K) [ +42.04695] and acetyl (K) [+42.010565] .

If I want to export 'Peptides' report from the Document Grid in the 'Peptide Modified Sequence' column, both can be seen as the same peptide if the 3-letter format was not chosen.

Could you please keep the rounding to the 2nd decimal digit?

Thank you,

Nick Shulman responded:  2024-06-12 08:34
You can create a custom report that has shows the modifications in a different format.
When you are creating a custom report, you can choose a column which is slightly different from the "Peptide Modified Sequence" column that you see in the default "Peptides" report.
One available column is "Peptide Modified Sequence Monoisotopic Masses" which shows the modification masses with as much precision as is available.
You can also choose "Peptide Modified Sequence Full Names" which shows the modification names instead of their masses.

If you would like to learn more about custom reports in Skyline you should look at this tutorial:
-- Nick
hassan hijazi responded:  2024-06-12 09:55
Thank you .