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Use cases

  1. A user launches the GUI, opens a mxML file, and browses through all the MS2 spectra to quickly assess their quality with the spectra view. He is interested on a certain precursor ion of, say m/z 567, subsets the data with [565,568], and looks more specifically at those spectra likely to correspond to his ion of interest. He then narrow the selection to [565.5,567.5], switches to XIC view and looks at the elution profile.

  2. A user has spectra identifications to his MSnExp instance (featureData slot). He subsets the MSnExp instance to spectra corresponding to a peptide IEEELGDNAVFAGENFH and with an identification score > 50, and fires up the GUI to visualise the new instance with the peptides of interest.

Summary of main features

  • Supported input: mzData, mzXML, mzML through the mzR package and MSnExp through MSnbase. Input can be provided as an argument or open through a dialogue box (raw or rda/rds file for the latter).
  • Visualisation: navigation through MS1, MS2, ... spectra (spectrum view) or extracted ion chromatograms (XIC view).
  • Possibility to subset the data to be visualised.
  • We also need a GO TO feature. For example, if the user is visualising spectra at the beginning of the retention time, and wants to go the the very end, it would be very inconvenient to click on next until her reaches the other end. Optimally, it should be possible to click any where on the gradient to immediately visualise the closest spectrum. I guess we could also get this feature with a 'Go to' filed/button; that would be less elegant and would add more (too many?) fields/buttons on the (simple) GUI. Note that once we have this, it might not be too difficult to have mouse zooming working - but that's really optional.


The msGUI S4 method allows one to open an empty GUI, a raw file or an MSnExp instance.

msGUI() ## opens empty GUI

Graphical user interface

  • The tabbed view described below will be updated soon so that the XIC and spectra can be visualised together (assigned to driu)

Spectrum tab

  • Plot of an MS spectrum
  • Navigate through consecutive MS1 and/or MS2 spectra using next/previous buttons - spectrum info and plot are updated
  • Check box to allow users the specify desired MS level(s).
  • Subset spectra by:
    • by precursor m/z (MS2)
    • retention time (MS1 and MS2 spectra)
    • spectra index (MS1 and/or MS2)
    • Precursor charge
    • (may be also mass, to be able to select different charge states of the same ion)
  • Zoom in and out of spectra.
  • Information about full experiment (summary) and spectrum displayed.

XIC tab

  • Plot chromatogram/XIC for all or a subset of spectra (subsetting as above)
  • Navigate to next spectrum in retention time using next/previous buttons - spectrum info is updated
  • Subset the spectra to be used to plot XIC by
    • precursor m/z (MS2)
    • spectra index (MS1 and/or MS2)
    • Precursor charge
    • (may be also mass, to be able to select different charge states of the same ion)
  • Zoom in and out of XIC curve
  • Information about full experiment (summary) and spectrum @rt displayed.


The Open button opens a file dialogue to select a raw data files or serialised MSnExp instances. May be a Help button could open the vignette. There could also be an Options button to set misc options (see below).

msGUI tabbed mockups Mockup of possible GUI fulfilling the desired functionality.

GUI candidates

  • The first attempt
    • Tabs exchanged to menu items (for aesthetic reasons mainly - more for usability purposes, really)
    • Three MS levels used in picture, number of checkboxes in actual display would depend on data file
    • Since different Filter options may apply to different Views (XIC, Spectrum), some options would be greyed-out when not needed. Picture
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