TIMS TOF DDA `mass errors unavailable' in histogramm

TIMS TOF DDA `mass errors unavailable' in histogramm sarah lennon  2021-04-15

Dear Skyline team,

I have loaded some TIMS TOF PRO PASEF DDA data into Skyline Daily and have extracted the M, M+1 and M+2 precursor ions for a list of 43 000 peptides. I would like to display the mass accuracy histogram but Skyline is saying :'mass errors unavailable'. The mass error is well displayed on top of each chromatogram.
I had no problem with DIA PASEF data.
Please find enclosed all the parameters I have used to load the data and a screenshot of the problem I am encountering. I might have done something wrong.

Thank you very much for your help,

Kind regards,

Nick Shulman responded:  2021-04-15
You can use the right-click menu on the mass errors graph to choose to display either precursors or products. In your screenshots it looks like you might have it set to only display mass errors for the products, and your document does not contain any product transitions.

You should right-click on the mass error graph and choose "Transitions > Precursors".

(It would be nice if Skyline automatically switched to showing precursors if you do not have any product transitions in the document, but it looks like we never did the work to make it that smart).

-- Nick
Brendan MacLean responded:  2021-04-15
At the very least, we should change the message to differentiate and clarify the mass errors of what are not available:

Precursor Mass Errors Unavailable
Product Mass Errors Unavailable

I think I have run into this one myself, and it is confusing. Definitely my first response was incredulity. Of course, they are available, I can see them in the chromatogram graphs, just like you, Sarah.

Sorry for the confusing UI.
sarah lennon responded:  2021-04-16
Hi Nick, Brendan,

Thank you very much for your very answer, I am all sorted now. I indeed did not think to check what was displayed.

Kind regards,