Wrong position of amino acids?

Wrong position of amino acids? fcsigloch  2020-01-13

Dear Skyline team,

I find the way of numbering amino acids of a protein in Skyline somewhat confusing: The first amino acid is given as position 0. This behaviour is especially misleading, when trying to locate point mutations or PTMs, where the Skyline position is reported to be one less than the normally reported one.

An example: if, say, a deamidation is detected on the first N of F2QME5 (see attached picture), it would be reported to be at position 3. But the N is actually amino acid #4.

Is this a bug or a feature of Skyline?


Brendan MacLean responded:  2020-01-13

Well, it was a bug that became a feature. It has been this way for over 10 years. Even when it was first reported several years into the development of Skyline, it seemed a little late to change it and possibly break anything that depended on the original implementations, which is my fault for being a programmer and using zero-based position, without realizing that 1-based is standard in the field.

Surprisingly, it doesn't come up very often. So, either not that many people are relying on it or those who do have just learned to adjust.

I am still not sure we can change this, given how long it has been this way, and even putting a setting somewhere like Tools > Options > Display could cause a lot of confusion unless we make every place we use the value (like the one you show in the Targets view) visually distinct (e.g. italics for either 1-based or 0-based, new format like [0: 0, 24] to show the base, ... something else)

It is definitely a known issue. We will consider your report a vote for providing an alternative, but it has been years since the last time this was reported. If others chime in with more votes to provide a 1-based alternative, that may increase its priority for us.

Thanks for taking the time to report it, and sorry that it causes some confusion. Definitely, if I had it to do over, I would have used 1-based. Sorry.


roberthardt responded:  2020-09-02


i would also strongly advocate for having a setting to change the numbering scheme. I frequently use Skyline to analyse PTM patterns on purified proteins and whenever I report the results to our collaborators they are confused with the -1 difference in AA positions.



Brendan MacLean responded:  2020-09-02

That's a good idea. We could probably add a check box or radio buttons to the Peptide Settings - Digestion tab.

Thanks for your feedback.