The Bubble Plot, also referred to as the Planetary System View, represents
a novel way of looking at one or multiple spectra at the same time. This view of
a spectrum still has the m/z value on the x-axis, but on the y-axis it has
the mass error (the distance between the theoretical and the experimental mass of the
fragment ions), and finally the size of each bubble represents the (normalized)
intensity of each fragment ion.
This way of looking at spectra takes a bit of getting used to, but once
one is comfortable with the setup, it becomes very easy to pick up details that
would have been very difficult to see by a manual inspection of individual spectra.
The size of the bubbles represent the relative intensity of the given peak. The bubbles
are automatically scaled to try to find the optimal bubble size, i.e., so that the bubbles
are neither too small nor too big. When using mass accuray in Dalton the scale factor
is 10 times the maxium mass tolerance (in Dalton), while when using relative accuracy, i.e., ppm,
the scaling factor is 1000 times the maxium mass tolerance (still in Dalton).
If the automatic scaling is not optimal, the scaling factor can be changed via the
Settings > 'Bubble Plot Scale' below the plot. Note that the value inserted here is
relative to the automatic scales above, i.e., entering a value of 2 will double
the size of the bubble (relative to the automatic scale), while a value of 0.5
will reduce the size by half (again relative to the automatic scale).
PeptideShaker automatically annotates the a spectrum with the
most likely ions given the spectrum and the peptide sequence identified.
This includes the automatic selection of neutral losses.
However, the user can override the default annotation by selecting
different ion types in the menu below the plot. To change the neutral
losses one first has to uncheck the Adapt option on the Loss menu.
To make sure that the same ion types are used for all spectra, the user
can also turn of the automatic annotation completly in the Settings
menu.
In addition to deciding which ion types to use when annotating the spectrum, the
user can also change the desired accuracy for the annotations. This is done by scrolling
the mouse wheel while holding down the Ctrl key. Scrolling up or down (when over the Spectrum panel) will increase or
decrease the accuracy required to say that a given peak should be annotated. The maximum value
is set to the fragment ion accuracy set in the Search Parameters dialog (found on the Edit menu).
Scrolling without holding down any keys lets the user decide how many of the peaks
PeptideShaker should try to annotate. The level is set relative
to the most intense peak, e.g., 80% means that the tool only considers peaks
that have an intensity that is at least 80% of the most intense peak. As
the value is reduced more and more of the low intensity peaks will be
annotated.
The bars highlighting and annotating the fragment ion types can be turned on or off by clicking the toggle names Bars.
The bubble plot has the potential of displaying multiple spectra at
once, and is automatically used if more than one row is selected in
the Peptide-Spectrum Matches table.
One more than one spetrum is selected the individual spectra are
annotated with the row index, and the fragment ions are color coded
accordingly.
Zooming is supported by the standard left click and drag approach, and additional plotting features can be accessed via the right click popup menu.