There is a link to the source file containing the isotope masses and abundances in the following support request answer:
https://skyline.ms/announcements/home/support/thread.view?rowId=65526
-- Nick

Hi Nick,

This is exactly what I needed. Thanks for pointing at the source.

If I understand it correctly, the masses currently used by Skyline to determine the mass of PTMs are the ones in the bottom (precision up to the 8th decimal), right?

I use the "Peptide Modified Sequence Monoisotopic Masses" output to correlate Skyline's results with outputs of other tools. Up until now I had not seen any issues with mass precision up to the 6th decimal. But with the massive mass of glycans I think the error is stacking up.

I am having issues on matching the "Peptide Modified sequence Monoisotopic Masses" as strings to those I was calculating using exact masses with slightly different masses past the 7-9th decimal to the ones in here (see attached Excel):

https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some

Is there a way to reduce the precision of the monoisotopic masses to the fourth decimal? E.g.:

IIISPEEN[+2789.999326]VTLTC[+57.021464]TAENQLER

change to ->

IIISPEEN[+2789.9993]VTLTC[+57.0215]TAENQLER

Or what would you recommend?

Sincerely,
Juan C.

Regardless of how many digits of precision are in the mass modification, Skyline never tries to match with more than 4 digits of precision.
There is a comment about that at the top of this source file:
https://github.com/ProteoWizard/pwiz/blob/master/pwiz_tools/Skyline/Model/MassModification.cs

Beyond four digits of precision, other tools do disagree with Skyline about what the mass of sodium and Carbamidomethyl are.

The way that Skyline decides that two modification masses are the same is controlled by the method in that source file called "Matches".
If the difference between the two mass values is less than .0001 then Skyline considers that the numbers are the same. This is almost the same as matching four digits of precision except in cases where the fifth digit might or might not round to "5" and thereby affect the way that the fourth digit rounds. For this reason, Skyline remembers six digits of the modification mass.

It sounds like you were hoping to be able to do some exact string matching on modified sequences.
The column "Peptide Modified Sequence" contains the modification masses rounded off to one digit of precision. Those strings can be compared exactly with other tools that also only keep one digit of precision.
The "Peptide Modified Sequence Monoisotopic Masses" column contains masses round off to six digits of precision.

Skyline used to only keep around 1 digit of precision, but sometime around 2017 more digits of precision were added so as to be able to distinguish Acetyl (42.010565 ) and Trimethyl (42.0469) as well as Formyl (27.994915) and Dimethyl (28.0313).

My advice is that if you want to modification masses to match as text, then you should only use the single-digit-precision masses that you find in the "Peptide Modified Sequence" column.
If you need to disambiguate modifications which match at the first digit of precision but differ at later digits then you will need to write code to do the complicate sort of matching that Skyline does of parsing the numbers in the square brackets in the modified sequences and checking whether those numbers differ by less than 0.0001.

-- Nick