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formed. For protein chemistry, this happens very often in order to get sequence
information for a given peptide ion selected in the gas phase. massXpert must
be able to perform those fragmentations in silico. Let’s see how an oligomer can
be fragmented using massXpert.
It is a matter of having a polymer sequence opened in an editor window
and selecting the sequence region to be fragmented. Once this is done, the user
selects the Chemistry−→Fragment menu. The user is provided with a window
where a number of fragmentation specifications are listed (Figure 8.19 on the
next page). As detailed for the cleavage of polymers, these fragmentation specifications are listed by looking into the polymer chemistry definition corresponding
to the polymer sequence of which an oligomer is to be fragmented.
The user selects the fragmentation specification(s) of interest, set the ionization range required for the generated fragment oligomers (the same as for
polymer cleave) and clicks the Fragment button. Upon successful termination
of the fragmentation reaction, the generated fragments are displayed in the
Oligomers table view widget.
As detailed for the cleavage of polymer sequences, the Details frame widget
displays data about the fragments generated and the way masses were calculated
for them.
Finally, one last note: if the list of monoisotopic or average masses are desired
in the form of a text list, right-clicking onto the table view widget will allow
copying to the clipboard either the monoisotopic or the average masses. Also,
it is possible to either export the data to the clipboard or to a file or even to
drag the displayed oligomer items in a text editor.
For oligomer data filtering, please refer to section 8, page 96.
Mass Searching
It may happen that the scientist needs to know if some arbitrary sequence region
would have a given mass. massXpert allows for mass searching operations in the
polymer sequence. This is done by using the menu Chemistry−→Mass Search.
The window illustrated in Figure 8.20 on page 95 shows up and the user enters
masses to search for. A number of parameters are to be detailed:
Q
Targets The masses should be searched for in the whole sequence or in the
currently selection region?
Q
Ionization When calculating masses for the potential oligomers matching
the searched mass, should different levels of ionization be calculated. For
example, one find in an electrospray ionization experiment mass spectrum
a peak at m/z 1245. It is not possible to know the ionization level for
that ion. On could imagine that this value is for a monopronotonated or
for a multiprotonated species. If we wanted to asses this, we might ask
that the mass be searched for by computing a range of possible ionization
levels between Start 1 and End 4 (admitting that for that experiment this
is what one would expect).
Once the masses have been searched for, if results are found they are displayed
in the same window in the Oligomers table view widgets (the left one for the
mono masses and the right one for the avg masses).