The Main Window 1: Import MGF files
The first page on the main window is used for selecting the datafiles that are to be searched.

Start selecting the files by pressing one of the buttons describing a type of fragmentation:

CiD/HCD, ETD, CUSTOM or Released glycans, and then pick the file(s), which must be in .mgf format.

You can search as many datafiles in one batch as the RAM in your computer allows, and you can mix fragmentation modes any way that you wish.

The "CUSTOM" option lets you define the fragment ions to search for. This can be useful when you use a dataset with combined fragmentation mode, such as EThcD, where the same scan may contain both b/y/c and z ions.

The "RELEASED GLYCANS" file option is used in conjunction with glyco-profiling. There will be more on this in the chapter on glycosylations.

MassAI keeps track of the selected mode for each file, and highlights this in the column marked "Fragment mode"

 
If you search a batch of datasets obtained under a variety of different conditions (īsuch as Ca concentration, temperature, pH), you can write these
into the "Conditions" column, and the condition for each datafile will be also be reported for each identified scan. You can then sort the results
based on the conditons, which makes it easier to compare results.
You can work with two sets of residue masses simultaneously, called set 
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.
(This can be changed on page 4 in the main window).

You can specify the set of masses for each datafile in the "RESIDUE SET"
column. Default is A. If you have a dataset where you have  both 14N and
15N labelled proteins, simply specify the value as "AB".
Once you have made a selection of datafiles they are listed in the above table, along with any specifications that you may have added, but per
default they are not loaded into memory until you start the actual search.

However, if you want to work with the files prior to searching, you can load them by pressing the "LOAD FILES NOW" button. MassAI will then
load the files and automatically display the "Precursor window" (below), from where you can work with your precursors in detail.
This feature is explained in a separate chapter.
Having selected the datafiles for your search,you should now move to the second page in the main window,
called: "2: Select proteins to search".