PeptideShaker supports two types of ion tables. The standard one with the theoretical fragment ion m/z-values, and a novel intensity based approach. The default is the intensity based. To display the standard ion table go to the Settings menu.
The novel intensity based ion table still shows you the fragment ion
covered by the spectrum, but instead of just showing the theoretical
fragment ion masses for those ions, it shows the experimental intensity
of the ions.
This new approach makes it very simple to not only see which fragment
ions are found, but also at which intensity (compared to the other
detected ions).
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 table. 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 novel intensity based ion table also makes it straightforward to compare the fragment ion coverage of multiple spectra. By simply selecting multiple rows in the Spectrum-Peptide Matches table the average intensity and standard deviation is shown for each fragment ion. In this way the stability of a given fragment ion can easily be detected.