Sq pk programming

Pika

To Do ASAP

• • warn clearly that this is done locally

• Have a mask to do integer masks (pika needs to check for dependencies... automatically adds dependencies) - no go because this is difficult

• Add a button in PeakHeights graph to jump to next run in todo

Keep all user settings from step 4

• Checkbox for truncating sticks to zero in stacked graphs.

• Default checkbox for when peak height <0, refit and constrain values < 0 to be 0 - checkbox on main panel - done

• Add squirrel baseline to PeakHeight graph... add left and right squirrel integration region - done

• Bug: When fitting open and closed separately, the residuals don't plot. - fixed

• Param graph

• • In many param graph, add small raw spectra insets to left and right

• • In many param graph, add radio buttons for raw and percent

• • In many param graph, add print all cursors

• • In many param graph, add graph showing spectra-like data with window highlighting where you are

• In peak shape do 3 things:

• • add option to truncate at 3.5 sigma

• • trim wings to ensure monotonicity

• • add option to subtract sq baseline from peak shape algorithm

To Do (Less Urgent)

• Add ability to duplicate PeakHeights graph and functionality (less urgent)

• In the m/z calibration panel, currently the width and accuracy vs m/z graphs don't show a summary of all the runs. E.g. the summary of all the peak widths for all the runs with error bars in the peak shape panel very nicely summarizes this information.

• We need to add camels, dromedaries, and vw "bug" ions to the lists. We need some notation for these ions, let me suggest vw28, vw23, d28, d32, and c28, c32, with the comment column describing what they are. It is important that those are lowercase letters, so people don't confuse these ions with vanadium (V) and tungsten (W). (less urgent)

• There is a need to consolidate the three sets of m/z lists that exist into a single one. We currently have the list of m/z possibly used in fits,(1) ones actually selected for HR sticks (2) list of m/z used for m/z calibration, and (3) the list of isolated ions. Each list is a subset of the previous one, and we can work with a single big list, and a series of masks to select / deselect the various m/z for the different purposes.

• Jose's new residual monster panel - high priority

To Discuss

• Change saving of the HR sicks matrix from masses that were selected to fit to all known masses.

Squirrel

To Do ASAP

• Query Wavemetrics about copy past functionality for panels
• Mike's pcurser in todo wave names

To Do (Less Urgent)

• We also need to be able to select some ions to be used in m/z cal and peak shape for V or W only.

To Discuss

• Changing frag table to reflect info in Allison's paper