Sq pk programming

Pika

To Do ASAP

• Change in step 4 options, test for peak height to be less than 0 to be less than user defined value (done in 1.03D)

• Warn clearly that changing selected masses is done globally (done in 1.03D)

• Add a button in PeakHeights graph to redo pika fits (Keep all user settings from step 4) (done in 1.03D)

• Checkbox for truncating sticks to zero in stacked graphs.

• Param graph
  • add small raw spectra insets to left and right
  • add radio buttons for raw and percent (Done in 1.03D)
  • add print all cursors (Done in 1.03D)
  • add graph showing spectra-like data with window highlighting where you are
  • have run numbers update with cursor move

• In final peak shape graph add ability to:
  • truncate at 3.5 sigma
  • trim wings to ensure monotonicity

• In final peak width/shape add ability 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.

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