smith-chem-wisc / proteoformexplorer Goto Github PK

Need to make a wiki and vignettes to describe functionality

• User should be able to right click a peak in the spectrum and view its XIC
• User should be able to specify a mass and charge, or m/z, along with a RT to view an XIC with its isotope peaks. Should be available in the species view and waterfall plot

Not sure what area to put this in yet, maybe it should be its own separate chart

Dashboard items should be inherited from a base class so that new types of dashboard items are easy to create/develop and integrate into the dashboard

• Font sizes, chart colors, etc. should be user-editable and saved to a text file
• Customizable deconvolution settings

need to add functionality to let users delete files

Put try/catch block around each plotting function so proteoform explorer doesn't crash, it should just display a popup error message

Automatically load results from proteoform suite into the dashboard, inside the proteoform suite GUI

For example, user can uncheck "identified" and identified envelopes would no longer be displayed, and the TIC chromatography on top would be subtracted by the identified TIC. this would make it easy to visualize areas that were deconvoluted but not identified, etc.

• TIC, % TIC deconvoluted, % TIC identified per file summary (dashboard chart)
• Number of deconvoluted envelopes per file
• Histogram of masses of deconvoluted envelopes per file
• Chromatogram and deconvoluted spectrum visualization
• XIC for annotated species and their charges/isotopes
• Cross-spectra file XIC 3d waterfall chart, for visualizing quantified differences between spectra files
• Proteoform family visualization (nodes and edges)

• User should be able to shift XICs in RT to manually align peaks
• User should be able to re-order files to group experimental conditions together, etc. for easier quantification visualization
• User should be able to switch between 3d and 2d views
• User should be able to change color of fill/line
• User should be able to remove fill if desired

GUI would present user w/ an envelope candidate, user can click a button to classify the proposed envelope. user could also create new classifications. over time the ML model would get better at deconvoluting envelopes and would propose cases it is uncertain about to the user for classification

https://github.com/AvaloniaUI/Avalonia

Upon loading TD results, there's supposed to be some peakfinding happening in the background to integrate TIC, etc. but this isn't happening yet

user should be able to create custom charts and save them to a text file for later use, i.e. if they want to chart all of a proteoform's isotopes in all identified charge states across RT, they could pick x=mz, y=intensity, z=rt

user could change layout of the dashboard, i.e. have a 2x2 grid or 4x2 grid of whatever charts are available

Currently centroid peaks are displayed. It would be nice to be able to visualize profile-mode data. This is probably relatively straightforward for Thermo .raw files, but since mzLib lacks functionality for reading profile .mzML, that part would be difficult.