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Scaffold 2.1

Scaffold Release 2.1.1
August 5, 2008

Mascot Data Storage

Scaffold will now allow users to download Mascot data from the server and analyze it at a later time. When downloading Mascot data from the server, we store the downloaded file in the sfd file until it is analyzed. Simply open the saved sfd file and run your Scaffold analysis without re-queuing the file.

 

Quantify and Similarity Lists

Protein drop-down lists now populated in Quantify and Similarity view.

 

Added GO Terms

New GO terms reported include: ER, Golgi, Endosome. Organelle Membrane.

 

Service Announcement
Scaffold Release 2.1.0

Beginning July 23, 2008, you may download the newest update of Scaffold − Version 2.1. The Scaffold 2.1 update includes multiple new features and bug fixes, plus enhanced data handling. As a result, Scaffold customer service strongly recommends that all users immediately download and install the software upgrade.

Here are some of the changes/enhancements in Scaffold 2.1.

Extended data parsing capabilities
Scaffold now loads data files from Spectrum Mill and OMSSA search engines, as well as SEQUEST, Mascot, X! Tandem, and Phenyx.

Fixed protein probabilities bug
Scaffold was previously underestimating protein probabilities.

Direct Mascot *.dat file loading
Scaffold can load *.dat files directly from the Mascot server.
This option is available under Edit > Preferences.

Fixed improper loading of Mascot *.dat files bug
Scaffold now properly loads Mascot *.dat files and correctly handles unassigned spectra.

Fixed data collation bug
Scaffold now correctly collates data from multiple search engines.

Enhanced structured directory loading
You can now load directories of data files which will be loaded into Scaffold as separate biosamples.

Scaffold 2.1 Support For OMSSA

Scaffold now includes support for the Open Mass Spectrometry Search Algorithm (OMSSA), an open source MS/MS search engine from the NCBI.

OMSSA normally reports only those identifications that are of high quality. In order for the Peptide Prophet algorithm in Scaffold to work correctly with OMSSA data, it is necessary to alter some parameters in OMSSA to output more of the incorrect distribution. We have included an example parameters file with Scaffold, "default.omssa.params.xml" in the "docs" directory of your Scaffold installation. You can load this file into the "OMSSA browser's" "Run OMSSA Search" tool. You can also add/change the following parameters on the OMSSA command line or in the XML file directly:

Disable the hit filter.
Command line: -ht 20
XML: <MSSearchSettings_tophitnum>20</MSSearchSettings_tophitnum>

Also, to maximize the number of false positives reported, set the evalue threshold high.
Command line: -he 100000
XML: <MSSearchSettings_cutoff>100000</MSSearchSettings_cutoff>

Unfortunately, these settings are not exposed in the publicly available OMSSA web interface by default.

 

 

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