March 2014 - Vol 6, Issue 1


Come visit us at these upcoming conferences

ABRF Booth #201. Albuquerque NM, March 22-25. ABRF web site

HUPO Booth #113. Seattle, WA, April 6-9. US HUPO web site

ASMS Booth #78. Baltimore MD, June 15-19. ASMS web site

ASMS User's Group will be held on Sunday afternoon, June 15. Sign up here.


New Scaffold and Scaffold Q+, Q+S features

In addition to fixing bugs since the Scaffold 4.1.1 release, we have added these features:

Scaffold Q+ and Q+S will show the protein clustering applied within Scaffold. Q+ and Q+S now support iTRAQ and TMT data from MaxQuant, TMT 10-plex and 8-plex, as well as dimethyl quantitation from MaxQuant and Proteome Discoverer. The masses of TMT 6-plex labels now correspond to the reagents currently distributed by Thermo. Additionally, you can display the Log2 fold change ratio comparing two categories.

In Scaffold we've added support for Proteome Discoverer 1.4 and its new Sequest HT search option. In Scaffold Batch, new tags were added for exporting Quantitative Values.

Don't forget... Scaffold Q+ and Q+S can read and display label-free, precursor intensity quantitation!

For the full details, see the release notes on our website


Check out Scaffold perSPECtives!

Scaffold perSPECtives, our newest tool, provides great flexibility in order to analyze large-scale proteomics experiments. You can categorize a massive number of samples using an infinite number of attributes. Easily summarize and re-summarize your proteins with your custom attributes to compare data and statistical tests in new ways. Cluster proteins hierarchically on expression profiles, sequence, and gene ontology to isolate classes of proteins that trend together.

Scaffold perSPECtives does all this with simple-to-interpret visualizations and powerful customization features. Watch video here.

Request an evaluation now!

For a description of the features, check out the perSPECtives brochure here.


We want to hear from you

What is one thing we could do better? Let us know!


Do you have a publication that cites Scaffold? Let us know!

We'll post it on our website and spread the word about your great work. Send us an e-mail with the details.


New White Papers, Documentation and Tutorial Videos

Our wiki includes introductory essays, white papers, FAQs, tutorials, videos, presentations, posters, citations and more! We've updated our information for loading files, including a new tutorial video and a compatibility matrix to easily identify which files are compatible with each Scaffold program.


In other news...

If you have any questions about Proteome Software or our products, contact us here.

Check our website for releases notes and bug fixes.

If you would like to sign up for product update notifications by email, click here and fill out the form on the right.


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Proteome Software, Inc
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Portland, OR 97219
Toll-Free (800) 944-6027