Some specific users are interested in seeing in Skyline:
* Potential interference - this is when some other peptide is contributing ions to the filtered Q1, Q3 pair. One of our collaborators published this paper with an algorithm for determining transitions where it is likely occurring (http://www.clinchem.org/cgi/content/abstract/56/2/291
* Auto-interference possible - this is when multiple product ions for the same peptide overlap in either the stable isotope labeled form or the unlabeled form, but not both, which can effect quantification. The best course of action is not clear yet, and may require data measurement to determine. In the current CPTAC study, operators are reticent to just give up ions with this potential, when the next best option may have much weaker signal, and the effect may actually be unnoticeable (e.g. y6+ and b12++ - the likelihood of getting any signal on a double charged b-ion that large is very small).
* Peak truncation - in scheduled MRM, you may not have captured the entire elution curve for a peptide. This should be a warning, so that users are immediately aware of how often this has happened in their results and can quickly navigate to view cases where it has occurred.
* Collision energy optimization failure to measure an apex value and too much variability in CE to peak area curve
* When using matched stable isotope labeled internal standards warn about outliers in peak area for the standard, which is supposed to injected at a constant amount. One recent email suggested 10x differences should be flagged.
I have decided it would be best to expand this and drive it off an expanded Find dialog.
To start, we could have it support the simple text find of the current find dialog, as well as add checkboxes for a few other interesting things to "find", like:
- Manually integrated peaks
- Truncated peaks
- Zero area peaks
- Annotated elements
The find dialog would get a check list with possible things to find, and a checkbox to show the results in the Find View. The check list would be populated from a list of "Finders" that implement an interface similar to what I have described before, and the Find View list would update as the document changed.