The Tool Buttons - Results Database
The result database is one way to save your results for later.
For each result, information is kept about the protein, peptide(s), modification, masses etc, along with the entire annotated scan, so
you can return at any time to retrieve the scans.
To use the database simply create or open a database from the file menu at the top.
You can then specify the minimum score in order to limit the results that will be saved into the database. In the example below we
have set the minimum to a score of 20.
You can select whether you wish to keep every scans for a specific peptide (or crosslink), or to only export the highest scoring
The later option is useful when you are preparing for a publication. This way, you can keep a database of only the top-scoring
In our example, we have opted to keep only the highest scoring scan per observation. You can see from the message window that
the same result has been observed with different scans when the results were saved. If the entry is already in the database with a
higher score, the new one is ignored. If the new scan has a higher score, the old one is replaced with the higher scoring one.
If in doubt, you can have one database which allows for redundancy, and another one for the top scans. In MassAI, you can have as
many databases as your harddrive allows, but only one can be open at a time.
You can always open and add new results to an existing database. You can open a database either prior to a search, in order to
include the saved results to your search space, or after the search for saving the results.
Click any result in the database to view the annotated scan
If you open an existing database prior to carrying out a search, you can tick the "use database in searches" checkbox.
This has the effect that MassAI looks through your database results for matching the scans included in your search as a first
resort, and secondly looks through other search spaces defined in protein selection.
You may have a number of specific details on the run conditions, that you wish to save along with your results.
In the database, you can assign any number of parameters to each file.
Default for a newly created database is five predefined parameter fields. The first two are always called "File" and
"Description", the remaining simply titled "Parameter" 1 to 3. You can rename the parameters by clicking the "change" button,
and you can add more parameters by clicking the "Add" button.
In our example case, we have renamed two existing parameters from "parameter 1" (and 2) into "Temperature" and "User".
The "File" parameter is filled in automatically, and we have then entered information into the description, temperature and
The above feature is very useful when you want to track under which circumstances you observe a specific peptide - or parts
thereof., you can then use the "Find peptide" feature of the database to look for a peptide sequence.
In the example below, we have entered the peptide sequence "KEEE" in the search field in order to see WHERE this sequence
occurs, and under WHAT circumstances.
Using a database in your search
You can include an existing database of saved results to search new datasets against.
This is generally much faster than searching through a (potentially) large search space, and can be combined with a
In this example, we have opened an existing database of saved results, which we wish to include
this into our search space. The "Use database in searches" checkbox is checked automatically when an existing database is opened.
We also define a larger search space in the "Select proteins" section of the main window, in this case, the human proteome.
When we start the search, MassAI intitially looks for matches to each scan in the result database. If nothing is found, the larger search space of the human proteome is taken into use.
A match is found for the scan to the right, and a peptide is proposed. (A)
A scan of the same peptide was also found in the database, and the top-scoring scan is automatically shown mirrored around the x-axis. (B)