Getting Started with Scaffold PTM

The following article contains a list of frequently asked question relating to getting started with Scaffold PTM. For specific questions not covered in our documentation we are available by telephone Monday through Friday from 8 AM to 5 PM PST. Our toll free number is 1-800-944-6027. Additionally support can be contacted via email at

Downloading Scaffold PTM

What is Scaffold PTM? What does it do?
Scaffold PTM is a computational tool that automates post-translational modification (PTM) site assignment in proteomic experiments. It analyzes MS/MS spectral output and provides researchers with an objective measure of the confidence of PTM (i.e., phosphorylation) site identification. Scaffold PTM uses Ascore’s probabilistic approach and scoring technique to annotate phosphorylation sites contained in MS/MS spectra.

Using Ascore, Scaffold PTM re-analyzes existing search engine results of previous searches done with SEQUEST, Mascot or other Scaffold-compatible search engines. The new analysis attempts to best match the observed spectrum for PTM site. It graphically displays a new list of reported PTM sites and the evidence supporting the assignment of the PTM to the site. By comparing site-determining ions, Scaffold PTM produces Ascore results assigning an ambiguity score to each reported PTM site.

The number of PTMs in each peptide can be determined by the precursor ion mass of the peptide’s spectra. Scaffold PTM adds this knowledge to the Ascore to derive a site location probability. Scaffold PTM then combines the site location probability estimates from all spectra matching peptides containing the site to obtain the best estimate of the probability that the PTM is at that site.

As a result, it reduces the amount of manual validation required while improving data set integrity. Accurate determination of these sites removes an important bottleneck in proteomics and facilitates faster and more comprehensive analysis.

Where can I get a free trial?
Free 14 day trials of Scaffold PTM are available on our website here.

How do I download Scaffold PTM?
You can contact our Sales department to discuss pricing. Scaffold PTM is available for download on our website here. Much of the installation and setup for Scaffold PTM is identical to Scaffold. For more information, see the Getting Started with Scaffold FAQs

Do I need Scaffold to use Scaffold PTM?
Unlike Scaffold Q+ or Q+S, Scaffold PTM is a stand-alone program that does not require Scaffold to function. However, Scaffold PTM can load mzIdentML exports directly from Scaffold.

Where can I learn about Scaffold PTM?
Besides the FAQ, you can also visit our Knowledge Base as well as the Scaffold PTM page on our website. Additionally the Scaffold PTM User's Guide can be found here

Batch Mode

Does Scaffold PTM have a Batch mode?
No at this time Scaffold PTM does not have a batch mode like the one found in Scaffold.

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