March 7th, 2011


Proteome Software


Proteome Software Releases Scaffold PTM

PORTLAND, OREGON - Proteome Software today released Scaffold PTM, the premier software for assigning
post-translational modifications to specific amino acid sites on proteins. Phosphorylation,
oxidation, deamination, acetylation are examples of the types of post translational
modifications that Scaffold PTM handles.

Scaffold PTM has algorithms that assign a site localization probability for each modification
and visualization features that allow confirmation of these assignments. Site assignments
from multiple mass spectra covering each peptide are combined to give the most complete
annotation of each protein's modification sites.

Scaffold PTM works in conjunction with most other bioinformatics tools (Mascot, SEQUEST,
X! Tandem, Spectrum Mill, OMSSA, Phenyx, PLGS2, and Scaffold) that process proteomics
data. The HUPO standard for data exchange, mzIdentML, is used to transfer data to
Scaffold PTM.

Data compiled by Scaffold PTM can be read by a free viewer. that anyone can download.
Free 14-day evaluations are available at

Proteome Software, founded in 2004, now has products (Scaffold, Scaffold Q+, ScaffoldBatch,
MassQC and now Scaffold PTM) in use in over 300 academic, public and private proteomics
research facilities around the world. The company’s headquarters is located in Portland,
Oregon and it has resellers in Japan, Taiwan, China, and the United Kingdom .

For further information:

Proteome Software
1340 SW Bertha Blvd, Suite 10
Portland, OR 97219
Toll-free: +1 (800) 944-6027