Hi Cristina,

I'll email you privately and we can arrange for you to get the data to us.

Brian Pratt

Thanks for providing your data. It required only a small change to the ProteoWizard code to support Agilent neutral loss scan data, it was just an oversight that it wasn't already supported. The fix should appear in the next Skyline-Daily, and in the meantime I will email you privately with a link to a special Skyline build that you can use to be sure that all is as expected.

By the way when you do go to create your Skyline document, I believe your transition Full Scan settings should be something like
MS1 Filtering
Isotope Peaks Included: None
MS2 Filtering
Acquisition Method: DIA
Product Mass Analyzer: QIT
Isolation Scheme: All Ions
Resolution: 0.7

and you will probably be interested in the "Product Neutral Loss" column for creating a convenient transition list.

Thanks for helping improve Skyline!

Brian

That's really great! Thank you a lot Brian and all the Skyline team for your work!

Cristina

You are very welcome!

But...

My colleague Matt Chambers points out that it's a bit more complicated than I thought, I expect it will be early next week that I'll have a full solution.

Best,

Brian

No problem about that from my side, thank you again for the support and the prompt feedback!

Hi Cristina,

Progress report: I've implemented a solution in Skyline, but it doesn't use the "Neutral Loss" column in transition lists. That's only a convenience for creating precursors to look for neutral losses in normal MS data.

You have "Neutral Loss Scan" data, in which Q1 values are reported only if a corresponding Q3 value is simultaneously detected with the m/z offset loss (or gain) of interest. The data can contain several different Q3 m/z offset values, each surveyed in rotation throughout the run. So we need some way to tell Skyline to look for the original precursor m/z, but only in scans that use the m/z loss of interest for that precursor/loss combination.

That's a perfect application for our recently added "Spectrum Filter" capability. Using the "Edit Spectrum Filter..." item in Skyline's Edit menu, I was able to create a copy of each of the precursor targets with a spectrum filter for each neutral loss the machine was programmed to investigate. Thus it was easy to see which targets had the neutral losses of interest and which did not.

I'll email you a link to a special build of Skyline for you to try out the new Neutral Loss option for Skyline spectrum filtering .

Thanks for helping make Skyline even more useful!

It is great that you implemented this, I have played with the template in the Skyline build you sent me and it works fine with my data.

Thank you a lot for your work!

Cristina