New features in Mascot Server 2.6

Spectral library searching

library search

This screen shot doesn’t show the results of a Mascot search of a Fasta file – it is a spectral library search using NIST MSPepSearch. Mascot search and library search are seamlessly integrated in Mascot Server 2.6.

When you submit a search, you can choose any combination of amino acid Fasta files, nucleic acid Fasta files, and spectral library files. When the search is complete, the results can be viewed and interrogated using the unique features of the protein family summary. This provides the advantages of rigorous protein inference together with grouping of related proteins into families.

In Database Manager, spectral libraries are handled symmetrically with Fasta files. Many public libraries can be enabled for automatic download, configuration and updating with a few mouse clicks. You can also schedule the automatic creation of spectral libraries from Mascot search results according to flexible import filters.

Other new features

FDR based on PSMs or sequences
You can now choose between counts of PSMs and distinct sequences as the basis for FDR calculation.
Extend Percolator calculations to all ranks
We used to pass only rank 1 matches to Percolator, and adjust other ranks pro rata. Now, all ranks are re-scored, so if Percolator decides that a rank 2 match is more reliable than a rank 1, it can exchange them.
Re-compress a database from Database Status
There is a new link in Database Status to re-compress a database. No need to stop the Monitor service and delete the *.stats file.
Default report shows only significant PSMs
Showing all matches unless you entered a score or expect value cut-off was confusing for many. Now, only significant matches are shown by default. If you prefer the old behaviour, this is still available by changing a mascot.dat setting.
Report p-values for fold changes in quantitation
See at a glance how reliable a fold change is.
Report mass delta relative to corrected mass for 13C matches
A small thing, but makes the report easier to read.
Private copy of Perl
Having to deal with annual releases of Perl, each binary incompatible with the previous, was becoming a nightmare. Mascot now installs a ‘private’ copy of Perl, so if some other software needs the latest version, or an old one, no problem.
Housekeeping
Mascot now includes a utility that can be scheduled to delete old cache files and compress old result files.

Mascot Daemon improvements

Daemon status filters

Export and import the task database
Either for backup or to make it easier to swap database engines.
Direct search submission
When Daemon is running on the Mascot Server, it will use command line search submission, bypassing the web server to avoid the 4 GB upload limit of IIS.
Better status information
The Daemon status tab displays more complete status information including percent complete and a button to allow a running search to be cancelled.
Tasks can be run serially
You can configure one task to start when another completes
Status tree can be filtered by date, keyword, database, etc.
If you have hundreds or even thousands of tasks on the status tree, this one’s for you.
Automatic export of quantitation XML
When using Distiller for quantitation
More flexibility for data import filters
Peak list files can be moved or renamed to handle utilities that use fixed paths or names

And, of course, an embarrassing number of bug fixes