any idea about the transitions of MFDCTNMPSPCHTK

any idea about the transitions of MFDCTNMPSPCHTK xinqun wu  2021-03-25

i want to use MFDCTNMPSPCHTK as a surrogate peptide to develop a quantitative LCMS method. get transitions (2+ or 3+ )from skyline suggested. but none of them showed the peak. MFDCTNMPSPCHTK has two cysteines and two Prolines, what modifications do i need to add into the structure setting?

Nick Shulman responded:  2021-03-25
If you send us your files we might notice something that might be going wrong.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:

It would probably also be helpful to see one of your raw files.
-- Nick
xinqun wu responded:  2021-03-25
I am new about the skyline. could I talk to you?
xinqun wu responded:  2021-03-25
I do not have files. i did denature and DTT reduction and iodoacetamide alkylation . what modification selection would be for cysteine?
Nick Shulman responded:  2021-03-25
By default, Skyline does apply the +57 Carbamidomethyl modification to all Cysteines. If you needed to make changes to that, you would go to:
Settings > Peptide Settings > Modifications

What type of mass spectrometer do you have? If you have a triple quadrupole, it might be a good idea to look at the Targeted Method Editing tutorial:

If you have a full scan mass spectrometer, it might make sense to look at the MS1 full scan tutorial:

I'll send you an email in case it's easier to answer your questions over email.
-- Nick
xinqun wu responded:  2021-03-25
I did that add on 57 on each Cysteine. no peak.
any other amino acid of MFDCTNMPSPCHTK will be affected after denature alkylation and reduction?