Proteome Software Newsletter

MassQC Standalone

Many of you started using our quality control tool, MassQC. All the benefits of the metrics can now be set up locally, in your lab. The new standalone version relies on your local server resources for improved performance. To learn more...

If you would like to give MassQC a try, please click the following link.

Scaffold's Grouping Algorithm

Protein grouping in Scaffold can be confusing to users. But it doesn't have to be. This article summarizes the way Scaffold handles grouping. Scaffold uses a protein grouping algorithm to reduce the number of proteins under consideration. Generally, this algorithm works by creating a table like that shown in the similarity view of Scaffold. Read more...

Configuring Protein Annotation Preferences

In Scaffold 3, a new feature, called Configure Protein Annotation Preferences, has been added to the Samples View. It allows an easier way of selecting the representative members of proteins families included in the list of identified proteins. The new feature acts globally on the list, allowing the user to set a series of preferences that will determine which family member will be viewed in the list. Read article...

Label-Free Quantitation with Progenesis LC-MS

Proteome Software is proud to announce it is a distributor of Nonlinear Dynamics' Progenesis LC-MS software. Existing Scaffold customers are eligible for a 10% discount on Progenesis LC-MS through March 31st, 2011.

In other news. . .

Many of our users process a large number of search results using our batch processing version of Scaffold. ScaffoldBatch is run from the command line and can process simultaneous jobs behind the scenes. Recently, the ScaffoldBatch manual has been updated with many additional commands. For more information about batch, check out the enhanced user's guide for more information...

Scaffold 3 is the industry standard in protein visualization and validation and reads the following files: Mascot (*.dat), Sequest (*.srf, *.dta/*.out, *.ms2/*.sqt), X! Tandem (*.xml), Phenyx (*.scaffold-pidres.xml), Spectrum Mill (each search result is a directory of files-load the whole directory), OMMSA (*.omx), Discoverer (*.msf), and Waters IdentityE (*.xml, using Scaffold Plug-in from the PLGS).