Adding FASTA Databases to Mascot/MaxQuant
Tutorial on adding FASTA Databases to Mascot/Maxquant on Windows HPC Protomics platform.
1. Global FASTA repository is located at:
(on parathyro login node)
C:\MassSpec\storage\db\fasta
which is mapped to a network drive:
\\troy.rc.fas.harvard.edu\MassSpec\db\fasta
Only admin users have write access to this folder.
If you have a tested database and would like to add it to a global/production repo, please request it at help@rc.fas.harvard.edu.
2. User databases
User-specific databases for experimentation/testing are located at:
(on parathyro login node)
C:\MassSpec\storage\db\fasta\users\USERNAME
which is mapped to a network drive:
\\troy.rc.fas.harvard.edu\MassSpec\db\fasta\users\USERNAME
if you do not have your USERNAME folder there, please request it at rchelp@fas.
NOTE: only privileged users will be able to do this, as even adding user databases requires access to Mascot administrative functions.
3. Steps to register the database using Mascot Web Interface.
a. Copy FASTA file to \\troy.rc.fas.harvard.edu\MassSpec\db\fasta\users\USERNAME
The fasta file name should be max 19 characters long (excluding .fasta extension) and should have a form:
DATABASENAME.fasta
or
DATABASENAME_MOD.fasta
or
DATABASENAME_VERSION.fasta
e.g.
uniprothum.fasta
or
uniprothum_frc.fasta
or
uniprothum_10.2.fasta
b. on parathyro, point browser to:
http://mango.seer.harvard.edu/mascot/x-cgi/db_gui.pl
(NOTE, you may need to login to Mascot WebUI first on the Home page)
c. choose a unique name for the database,
Look at the list of available names, choose a unique name for your database.
The name identifier for a user-database should start with USERNAME, i.e:
USERNAME_uniprothum_frc
d. Register new database in Mascot
From list of databases, select NEW_FASTA_TEMPLATE — this will load defaults.
Click “New Definition” button.
Enter:
- name of database in the format described above,
- path to the database in the format:
C:\MassSpec\storage\db\fasta\users\USERNAME\DATABASENAME*POSTFIX.fasta
or
C:\MassSpec\storage\db\fasta\users\USERNAME\DATABASENAME_*POSTFIX.fasta
The actual fasta file name must be max 19 chars (Mascot limitation).
Ensure the path is local c:\MassSpec\… path, not a UNC path to \\troy storage.
NOTE: the * asterisk is required by Mascot. It needs to match at least 1 character (POSTFIX), otherwise Mascot rejects it. This allows to bundle several database files into one “family”, but it’s also potentially confusing and we need to be careful not to match another unwanted database.
e. Keep the remaining default fields (e.g. parsing rules) unless you know they need to be changed for this particular database.
f. Click APPLY button.
4. At this point the database is registered, but it is still inactive. Mascot needs to test and index it first.
a. create a test file.
- Go to C:\MassSpec\storage\data\mascot\test
- copy file NEW_FASTA_TEMPLATE.asc to USERNAME_DATABASENAME.asc (or USERNAME_DATABASENAME_MOD.asc)
NOTE: USERNAME_DATABASENAME has to match the unique name of the database as registered in Mascot, not the name of the FASTA file.
- edit the new USERNAME_DATABASENAME.asc file (right-click, edit),
- change the line NEW_FASTA_TEMPLATE to USERNAME_DATABASENAME
- save and close the editor.
5. At this point, Mascot will read the test file, execute a series of tests and index the database.
6. In web browser (on parathyro), go to http://mango.seer.harvard.edu/mascot/x-cgi/ms-status.exe and verify the current status of the database.
After indexing, the status of the database will change to “In Use”, unless there are errors.