Spectrum View

The spectrum view is used to visualize nodes’ spectra.

Spectrum View Window

The left pane shows the loaded spectra. You can visualize up to two spectra for comparison. The top spectrum (in red) is the first one loaded while the second one appears upside-down in the bottom part (in blue).

On the top-right corner of the spectrum, you can see the computed similarity score between the two spectra. Value lies between 0 and 1, the higher it is, the closer the spectra are to each other.

On the lowest part of the window, the legend gives information about which spectra is shown (node index and m/z of parent ion).

Matching Peaks List

When two spectra are loaded, the right-hand pane contains information about which fragments or neutral losses are common to both spectra:

  • The top table list matching fragments,

  • The lower table is for matching neutral losses.

Each table has three columns:

  • Top Spectrum: m/z of fragment or mass of neutral loss in the first spectrum

  • Bottom Spectrum: m/z of fragment or mass of neutral loss in the second spectrum matching the one of the first spectrum

  • Partial score: Contribution of these fragments/losses to the overall matching score. These partial scores add up to the total score.

When a line in this table is selected, the corresponding peaks in the spectra are highlighted. Click anywhere in the table outside any cell to deselect all lines.

Toolbar

Spectrum View Toolbar

Spectrum View come with a navigation toolbar on top of the window, which can be used to navigate through the spectrum. Here is a description of each of the buttons:

  • home back forward Home, Forward and Back buttons are akin to a web browser’s home, forward and back controls. Forward and Back are used to navigate back and forth between previously defined views. They have no meaning unless you have already navigated somewhere else using the pan and zoom buttons. This is analogous to trying to click Back on your web browser before visiting a new page or Forward before you have gone back to a page – nothing happens. Home always takes you to the first, default view of your data. Again, all of these buttons should feel very familiar to any user of a web browser.

  • move The Pan/Zoom button has two modes: pan and zoom. Click the toolbar button to activate panning and zooming, then put your mouse somewhere over an axes. Press the mouseleft left mouse button and hold it to pan the figure, dragging it to a new position. When you release it, the data under the point where you pressed will be moved to the point where you released. Press the mouseright right mouse button to zoom, dragging it to a new position. The x axis will be zoomed in proportionately to the rightward movement and zoomed out proportionately to the leftward movement. The point under your mouse when you begin the zoom remains stationary, allowing you to zoom in or out around that point as much as you wish.

  • zoom Click the Zoom-to-rectangle button to activate this mode. Put your mouse somewhere over an axes and press the mouseleft left mouse button. Drag the mouse while holding the button to a new location and release. The axes view limits will be zoomed to the rectangle you have defined. There is also an experimental ‘zoom out to rectangle’ in this mode with the mouseright right button, which will place your entire axes in the region defined by the zoom out rectangle. You can also zoom in and out using the mousescroll mouse wheel.

  • save Click the Save button to launch a file save dialog. You can save as images with the following extensions: jpg, png, ps, eps, svg, pdf, pgf, tif, raw, and rgba. You can also save spectra as text in the following formats: mgf and msp.

  • reset The Reset button will simply unload any previously loaded spectrum.

Load spectra

To load a spectrum, simply select a node in view and use the View ‣ Spectrum menu or the S shortcut. You can also compare two spectra: select a different node and use the View ‣ Compare Spectrum menu or the C shortcut. Second spectrum will appear upside-down. Spectra can also be loaded from the nodes metadata table.

Shortcuts

Shortcut

Description

H, R, Home

Home

Left, C, Backspace

Back

Right, V

Forward

P

Pan/Zoom

Shift

Hold to temporarily activate Pan/Zoom

O

Zoom To Rect

Ctrl

Hold to temporarily activate Zoom To Rect

Ctrl + S

Save

g when mouse is over an axis

Toogle major grids

G when mouse is over an axis

Toogle minor grids