The Main Window 2: Select proteins
On this page in the main window, you define your search space in terms of proteins to include.
There are two ways to do this: The first is by supplying MassAI with a list of protein sequences as a text file in standard FASTA format.
Load this file by pressing the "L" button (highlighted in blue). The file can contain any number of protein sequences.

From the column on the left, you can select any of the proteins in your search space to view. The sequence is displayed in the center column, and any
pre-defined features of the protein are displayed on the right.

In the example below, we have imported a file containing 6 known glycoproteins. The middle column shows the protein sequence of serotransferrin. The
right hand window shows the known glycoslyated residues in the protein. The N-linked N432 is highlighted in light blue on the sequence.

Pre-defined features currently include domain descriptions, known PTMs, glycosylated residues and disulfide bonds.
Such modifications are automatically included into the search. If any protein contains pre-defined modifications, the corresponding algorithms for
handling these are turned on automatically, and will be limited to include the pre-defined modifications only.
You can turn off the automatic PTM search by unchecking the "Include in search" box  
You can add new pre-definitions to your proteins directly into the right hand column, or you can transfer them from the later list of search
results, by right clicking on a result and selecting "Add PTM to protein definition". (this will be covered in detail in a later chapter)
Add glycosylation to protein sequence
If you choose to add pre-defined PTMs to your sequence, remember to click "SAVE to FASTA" in order to keep the definitions for later searches.
The SECOND way to define a search space is to include one or more proteomes.
Each MassAI distribution comes with a copy of the latest UNIPROT databank at time of release, and each organism known in UNIPROT is listed in
the leftmost column. Include a proteome by selecting it on the list, or you can search for it, by typing in the name of it in the search field.
Then press the "->" button to move it to the center column for "currently included organisms".

You can browse through the included proteins in the rightmost column, and toggle proteins for inclusion/exclusion.
Now that you have defined your search space, you should continue to page 3 : Set search parameters