Proteome Software News...

>>> Release Notes

Our LC-MS Quality Control tool, MassQC 1.7.2, is available as a standalone application. See below...

Scaffold 3.1.4 has been released. Evaluate for 14 days here...

Scaffold PTM 1.1.3 has been released. Evaluate for 14 days here...


Hint of the day:
Did you know? You can create customized Gene Ontology databases for Scaffold.


MassQC Standalone LC-MS Quality Control Software

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.


Custom Gene Ontology Annotations

A number of Scaffold users have asked about the possibility of developing customized Gene Ontology databases. Perhaps you are curating a database for a particular species, or you have downloaded GO information for a certain taxonomy but it is not in standard GOA form. Scaffold can easily accommodate such custom sources of GO information. All that is required is to create a properly formatted Excel spreadsheet and to direct Scaffold to use that file as the source of its GO annotations. Read more...


New Discoverer MSF Features

Since many of our customers are beginning to use Proteome Discoverer 1.2 or 1.3 more consistently, we found ourselves needing to face and resolve some issues related to the way Scaffold reads and interprets data contained in the MSF files created by Proteome Discoverer. Some of the issues, experienced both by our customers and us, have been addressed through a fair amount of implementation developed in the 3.1.4 version of Scaffold (available for download on our website), the most noticeable improvement being the ability to load MSF files with multiple processing nodes (e.g. CID and ETD data). Read article...


Enhanced ScaffoldBatch Features

Many users use ScaffoldBatch to process large numbers of files in a high-throughput manner. Some have sought assistance with the use of Sage-N's Sorcerer. Sage-N and Proteome Software have been business partners and collaborators for many years. Recently, we have made some progress with batch processing and the Sorcerer users will now get to benefit from these enhanced features. For more information...


In other news. . .

Many users often encounter how memory (RAM) plays a significant role in Scaffold. As an application that uses the Java Virtual Machine (JVM), Scaffold relies heavily on memory to process results and hold those results for immediate manipulation and visualization. This is why it is very important to remember to allocate your memory in the Preferences section under Edit in Scaffold.

Also, don't forget that Scaffold PTM runs in batch mode too, similar to ScaffoldBatch for Scaffold and Scaffold Q+. Read through the users manual to see how and to learn some introductory commands.

Some of you may know that we are selling Nonlinear Dynamics' Progenesis LC-MS for label-free quantitation. Well, we recently agreed to distribute Sierra Analytics' HDExaminer software for HD exchange.

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), Proteome Discoverer (*.msf), and IdentityE (*.xml, using Scaffold Plug-in from the PLGS).

If you have any questions about Proteome Software, Scaffold/Scaffold Q+, Scaffold PTM or MassQC, contact us here. Check our website for releases notes and bug fixes.

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Proteome Software, Inc
1340 SW Bertha Blvd, Suite 10
Portland, OR 97219
Toll-Free (800) 944-6027