I think you should make the second residue in the peptide "A", and apply a modification with the chemical formula "CH2" so that it ends up being transformed into Aib.

From what I read online, the peptide has the sequence:
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRG
and it has the chemical formula C187H291N45O59, so I think you need to put the CH2 on the first "A" and then put a modification of C35H61N3O12 on the "K".

If you want to see the chemical formula of a peptide, you can create a Report in the Document Grid which includes the "Molecule Formula" column.
If you would like to learn more about Custom Reports and the Document Grid you should look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

If you would like to learn more about working with modifications in Skyline this is the webinar that we recommend:
http://skyline.ms/webinar10.url

-- Nick

Hello Nick,

Thank was very helpful. I was able to adjust the modifications. However, I am seeing 4112.1227+ which is not exact considering the molecular weight of 4113.5775. Could you inform me of any factors that might have caused this mass error? I have attached the file.

4112.1227 is the monoisotopic mass of the molecule plus one proton because it's charge +1.

I believe the molecular weight 4113.5775 that we see online is the average mass of the neutral molecule.

If you go to:
Settings > Transition Settings > Prediction
and change "Precursor mass" to "Average", then the m/z that you see displayed in the Targets tree changes to "4114.6129", which is pretty close to one proton heavier than that 4113.5775 number.

With high resolution mass spectrometers, you nearly always want to monitor the monoisotopic m/z instead of the average mass m/z, so you will want to set the "Precursor mass" to "Monoisotopic".
-- Nick

That's really helpful. Thank you so much.