The Main Window 4: Select modifications
On this page you define the modifications to be included into a general search.
You will find four sub-pages here, to cover standard modifications, cross-linking, glycosylation and labelled residues.
If your proteins have pre-defined modifications (see protein selection), they will be included automatically.

Hydrogen-deuterium exchange is not considered a modification per se, and is handled elsewhere.

The first sub-page contains a selection of fixed and variable modifications.
You can select as many as you want, and set a maximum limit to how many modifications to allow on each peptide.

Oxidised methionine and cysteine alkylation are selected per default.
You can edit in the lists and add/remove
modifications by pressing the button marked
"E" (edit). This  opens a built-in text editor,
where you can modify any of the text files that
come with MassAI.
On the second sub-page you can define the search parameters for a cross-linking experiment.
This includes one (or more) cross-linkers, search algorithms and limiters.

There are four different search algorithms for cross-linking. XODYS is the most recently developed algorithm. It is the faster of
the four, but also the most demanding in terms of scan quality. CROSSWORK is slow but picks up cross-links in scans of poor
quality. These two are selected per default.

Crosslinking and working with the result output is covered in detail in a separate chapter on cross-linking.
The third sub-page handles the identification of peptide glycosylations.
Compared to cross-linking, the settings for the glyco search are more complex, as peptides and glycans fragment
differently according to the fragmentation method.

You start by selecting the glycan library to work with. Currently the following groups are included:
All known glycans, mammalian cells and yeast. It is easy to define your own group by pressing the edit button marked "E".

MassAI handles datafiles from both intact glycopeptides as well as released glycans. You can select datafiles from both
types during "file selection", and MassAI will automatically annotate, whether a glycan has been observed both in its free
form as well as attached to the peptide.
MassAI contains several features for glycomics, which will be described in detail in a separate chapter.
On the fourth sub-page, you can define two sets of residue masses, which can be included in a search simultaneously.
These are referred to as sets A and B. Per default, set A is the standard N14 masses of the 20 common residues, while the mass values
for set B are set as N15 labelled residues.

When you select your datafiles, you can specify the set of masses belonging to each datafile. Default is A. If you have a dataset where you
have  both 14N and 15N labelled proteins, simply specify the value as "AB".
This concludes our tour of the main
window, and you are now ready to start
the search.