Scaffold Software Solutions
Proteome Software offers a variety of proteomics, metabolomics, and small molecule mass spectrometry software solutions for handling large-scale, data-rich biological identification or quantitative experiments. We innovate on the leading edge of MS/MS analytics, and our software tools are used in hundreds of laboratories and universities around the world.
Free viewer Collaborate and share results using the cross-platform Free Viewer for all the Scaffold Software tools. Select a product below and click the installer you need on the left side. Without a license, all our tools function as a Free Viewer.
The Industry Standard DDA MS/MS Proteomics Tool
Search raw data directly with MS Fragger* integration and load precursor intensity data from FragPipe
A Full Suite of Tools for Labeled and Precursor Intensity Quantitation
Quantify proteins using iTRAQ, TMT, SILAC, and precursor intensity values
The Look and Feel of Scaffold, the Power of DIA
Search raw DIA data against various DDA library formats, Prosit predictions, or sample-specific DIA-only custom libraries
Experiment-driven Labeled and Label-free Quantitative Analysis
Analyze iTRAQ/TMT data from Proteome Discoverer, Mascot, or PEAKS mzIdentML files or label-free/isobaric-labeled samples from Scaffold
Scaffold Software Meets Small Molecule LC-MS Analysis
Identify and quantify small molecules using MS1 or MS/MS data
Illuminating the World of Protein Post Translational Modifications
Evaluate modification site assignment confidence using Ascore and Ascore-derived probabilities
Managing a core facility or shared resource department? Need help with gaps in your software pipeline? Want to try new methods like DIA proteomics? Do you need a free and easy way to share results with your customers?
Need an elegant yet easy to use solution for data processing? Not sure where to begin when starting up a new lab. Let us help take the pressure off setting up a software pipeline so you can focus on the science.
Tutorials & Videos
Check out our YouTube channel for Scaffold tutorials, from getting started to advanced use. We have videos for all our Scaffold products, as well as videos from previous conferences and special events.