The Tool Buttons - Result scans
This window presents a list of the search results, scan by scan.
The window appears automatically once a search has completed (along with the PROTEIN result window), and also when you press the
SCANS button from the tool button window.
The window layout contains a series of sub-pages, each of which displays a specific type of result (A).
These are: Standard peptides, peptides with modifications, cross-linked peptides, glycopeptides and their corresponding released
glycans, results below the currently selected minimum score and results gained through the various data-mining features

The column to the right (B) contains checkboxes, which show or hide the individual data-columns.

You can sort the dataset by any column, simply by clicking on the headline of each column. Click once for ascending values, twice for
descending. A small, triangular arrow next to the headline shows which direction is currently active.

 
A
B
In the above figure, we have sorted a result dataset by
its score in descending order. The currently selected
entry is highlighted in light blue, and its corresponding
scan is shown automatically, along with all
annotations. You can navigate through the table by
mouse clicking, or by using the up and down keys on
your keyboard.

If you close the window containing the annotated scan,
you can always reopen it by clicking the "SPEC"
button in the tool button window.

The annotated peptide sequence is opened by
clicking the "PSEQ" button in the tool-button window.
Below is the table of results containing peptides with some type of modification. In this case, we notice that most of the modifications
are dead-end cross-links. This is when the selected crosslinker (BS3) reacts with one peptide, while the other end of the cross-linker
has reacted with water or a non-peptide free-amine.
Notice that dead-end cross-links are not considered "proper" cross links, and are treated as a peptide with a variable modification
instead.  "Proper" cross-links are reported separately in the table entitled "Cross-linked peptides"
This is the table which lists all the identified peptide cross-links. 
This table has a few additional columns that you will not find in the other tables. These include additional proteins/ peptides B and C,
along with notes on the algorithm used to identify the cross-link.

The "Scan Number" column stands out from the other columns, as the text has a colour.
A green colour signifies that this is the highest scoring result for this particular scan. A red colour signifies that there is another result to
the same scan, which  has a higher score. For a scan to have more than one possible match is commonplace when working with
cross-linking. One of the peptides in a cross-link, usually the longer one, or the one comprising the most aliphatic residues, tends to
fragment more intensely than the other peptide. This makes it easy to identify and validate the "A" peptide. On the other hand,
Identification and validation of the more poorly fragmenting "B" peptide often relies on mass and very few fragment ions.
On the lower half of the cross-link subpage, you will also find the two tables below.
Table A presents the same results as the main table. Only, in table A have the individual results been collected into unique cross-links,
which are the represented by a number of observations.

In this case, we show the results found in a data file from a cross-link experiment. Two different types of cross-linker was used: BS3
and the quadruply deuterated BS3-d4. Furthermore was the experiment conducted under two different conditions: with and without
added EDTA. You can see which cross-links are observed under which condition in the "Condition" column. In the example below, we
have picked a cross link from the EDTA and BS3-d4 treated sample. This particular cross-link has been observed in five different
scans, which are listed in the rightmost table.
Selecting any of these brings up the anntated scan.