Sq pk programming

Pika

To Do Priority

• Create other methods for the user to select masses to fit beyond the simple default option.

• The legend for the peak width graph doesn't update when defaults are changed.

• Checkbox for truncating sticks to zero in stacked graphs.

• Param graph
  • add small raw spectra insets to left and right
  • 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

• In Peak shape panel the first run number of index should be put into “run number” field (it defaults to 0)

• Prepare for release of O/C Panel at Manchester Users' Meeting
  • Coordinate with Allison for code and panel
  • Prepare example dataset and tutorial

To Do (Less Urgent)

• Step 4 of pika: maybe rather than two options (one run or Todo wave) and one button, we could just have two buttons? Something like “Calculate HR Sticks for averaged Todo wave” and “Calculate HR Sticks for one run”?

• Add ability to duplicate PeakHeights graph and functionality
• 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.
  • (Jose) This could be done with a radio button on top of the graph that selects SR/AR (meaning single run / all runs)
• 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), tungsten (W), and deuterium (D).
• 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.
• change the field analysis to warn users to check for large CO influence in ab correction; provide a sample pre and post AB correction from Tim to demonstrate
• change frag_organics as per Allison's paper
• change frag_sulphate as per Ann M's paper
• (Jesse) changes to default HR masks...remove all organic peaks with 2 nitrogens from default list; ones to add include 33SO, and all j13CC(x)H(2x+1) peaks

To Discuss

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

Done

• 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)
• Partition Avg ability for todo waves (especially v only, for Qi Chen - done in 1.03A)

• In Param graph add radio buttons for raw and percent (done in 1.03D)
• In Param graph add print all cursors (done in 1.03D)
• Add button for web link in credits panel. (done in 1.03E)
• In the graph for one spectra HR fit, move the redo fits button so it is farther away than the arrows. (done in 1.03E)
• Double check m/z parameters (so they are not nan) before trying to fit (done in 1.03E)
• Alex had an issue with the show inset button being clicked on, but the insets weren't showing up. Make sure that this toggle value keeps up with the display. (done in 1.03E)

Squirrel

To Do Priority

• Mike's pcurser in todo wave names
• Changing frag table to reflect info in Allison's paper (in next release, coordinating with Jose for sending email to the users)
• Bug found by Mike Q about checking modifications of all frag waves, not just species selected in average mass spec
• Bug found by Carly whereby the MS time series for the species all can replace the 'all' todo wave
• Make more consistent the todo wave creation scheme whereby users can input "todowave and not 1xxx and not 2yyy" for the todo wave formula
• Mike Q's issue with m/z calibration with fast mode data
• Time O's issue with somehow getting the squirrel_index matrix messed up and getting the stick matrix data set being as wide (columns) as the raw spectra matricies.
• When a user enters runs and the first is > than the last, 45-40, a better error message should be generated.
• Pre-process: when recalculating sticks with new m/z parameters, the error related to some m/z parameters being NaNs often shows up. A few times at the beginning, and then halfway through. Is there any way to deal with this more effectively?
• From Jesse: ptof output: ug/m3 isn’t the right y-axis
• In the baseline subpanel, make the mass defect default values more clear.

To Do (Less Urgent)

• In the baseline panel allow uses to go higher than m/z 500.
• Should we allow users to enter a negative value for the PToF vl parameter?
• MS: plotting non-consecutive runs (for example, allV when you switch between V and W) gives a blank plot, because “Gaps” is the default for plotting “lines between points”. Is there a way to remove the “gaps” option so the data plot right away?

• Occasionally after preprocessing, the status bar ends saying “Estimating space requirements” rather than “Done”

• For DC marker corrections, Manjula wants to be able to enter nitrate, and then have squirrel figure out what m/zs this corresponds to.
• In average mass spec graph, when checking linear scale have the default go to 0.
• In average mass spec graph, check the display of negative values. (Doug thought that it wasn't working right.)
• In average mass spec graph, perhaps add a 'magnification' drop down menu - x 2, x 10, x 25, etc.
• Possibly rename the checks to be done before preprocessing as 'stick adjustments'.
• Change defaults in Frag checks tab to be 'all' and colored by timewave.
• Fix bug that pops up in Frag checks plots.
• Doug really likes for tables to have columns be the minimum width that is sensible.
• Re-look at IE/AB calculations.
• Doug really likes to have time series graphs be such that grids are on midnight of every day, and labels have day of week inserted.
• In the diagnostic plots, perhaps the PToF airbeam wave should be nanned whenever the run doesn't have PToF data.
• In m/z calibration panel, check the possible bug when interpolating across a todo wave.
• Ask user to save experiment before blacklisting and/or indicate how to unblacklist
• In diagnostic plots, change legends that give integer m/z values to molecular species.
• In the m/z calibration panel, when doing one run, override live update checkbox.
• We need to be able to select some ions to be used in m/z cal and peak shape for V or W only.
• Review todo wave name length limitations.
• When doing an m/z cal fitting, put runs with bad fits into a separate todo wave.
• In the m/z calibration panel, make more clear what the nan param button does.
• From Tim O:During manual (F3) saves, the mass spectral data (e.g. MSOpen_V, MSSOpen_V, etc.) are saved as simple data arrays with the m/z in the rows direction. During autosaving, even if only for one run, these waves are always saved with the m/z in the column (run number in the row dimesion). It turns out that Squirrel can read and process either, just not at the same time. Thus, while he can process the data separately, he cannot ask Squirrel to load and process autosaved data with nonautosaved data interspersed.
• Incorporate some peak finding code as per Jesse's request
• Deal with Fast runs truncatings
• Update squirrel web site
• From Ken: In the baseline fitting panel make the main plot in the popped window automatically scale the x axis to that in the main window.
• From Ken: In the baseline fitting panel, when scrolling through the baseline fits for all runs in a todo list, add the ability to pause on a chosen run. It would also be great to select the direction in which the run baselines are scrolled - forward or backward.

To Discuss

• Change frag table of sulfate according to suggestion from Ann
  • Current frag_sulphate -> frag_sulphate_old
  • New frag_sulphate doesn't depend on frag_SO3 and frag_H2SO4 (Ann will wori up this new table)
  • Frag_SO3 and H2SO4 are kept in Squirrel for reference and if someone wants to put them back to use, but not used by default