Can you give us the transition list file that you imported?

Transition list in the attachment. Let me know if you need any additional information.


Thanks,
Yi

Thanks for sending us that transition list.

If I understand your problem correctly, it's that you have this in your transition list:

Precursor Name    Precursor m/z    Product m/z    Precursor Charge    Product Charge    Molecule List Name    Product Name
CL96-169    684.351334    422.239796    4    1    cross-linked peptide    A y3+
CL96-169    684.351334    537.266739    4    1    cross-linked peptide    A y4+
CL96-169    912.132687    422.239796    3    1    cross-linked peptide    A y3+
CL96-169    912.132687    537.266739    3    1    cross-linked peptide    A y4+

However, when you import that transition list into Skyline, the number 912.132687 gets changed to 912.4686.
Also, the two transitions that belong under 912+++ get put into separate precursors.

My guess is that the reason Skyline is doing this is that
4/3*684.351334 = 912.4686

I will ask around on the Skyline team about whether this is the correct behavior.

Then there is a mistake in the calculation, since the precursor masses are different for two charge states (different by 1 Da)

It should be the following: (684.351334*4-1)/3 = 912.132

Hope this helps.

Hi Yi,

The problem is that "charge" is ambiguous - in this case, it implies protonation, but that's not the only way to charge a generalized small molecule. Of course it's a very likely way, so we really should be able to guess at this (and will work on doing so), but for now try it with explicit ionization descriptions instead:

Precursor Name    Precursor m/z    Product m/z    Precursor Charge    Product Charge    Molecule List Name    Product Name
CL96-169    684.351334    422.239796    [M+4H]    1    cross-linked peptide    A y3+
CL96-169    684.351334    537.266739    [M+4H]    1    cross-linked peptide    A y4+
CL96-169    912.132687    422.239796    [M+3H]    1    cross-linked peptide    A y3+
CL96-169    912.132687    537.266739    [M+3H]    1    cross-linked peptide    A y4+



Thanks for helping improve Skyline!

Brian Pratt

Thanks! The transition list now can be imported. However, there are two other problems.

1. Some of the molecules are recognized as heavy labeled but they are actually not (for example, CL96-169 -> 912.1327).
2. I can't found the precursor option for the small molecules (it is available in the proteins part)

Could you help me to take a look? Let me know if you need any additional information. Thanks.



Yi

>> 1. Some of the molecules are recognized as heavy labeled but they are actually not (for example, CL96-169 -> 912.1327).

Not sure why that's happening (but I will find out!) - you can clear that manually in the Targets tree though.

>> 2. I can't found the precursor option for the small molecules (it is available in the proteins part)

Sorry, I don't understand the question. Can you be more specific?

Brian