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.

Scaffold 5

Scaffold 5

The Industry Standard DDA MS/MS Proteomics Tool

Search raw data directly with MS Fragger* integration and load precursor intensity data from FragPipe

*MS Fragger license required; free for academic labs
Scaffold Q+S

Scaffold Q+S

A Full Suite of Tools for Labeled and Precursor Intensity Quantitation

Quantify proteins using iTRAQ, TMT, SILAC, and precursor intensity values

Scaffold LFQ

Scaffold LFQ

Simple, Experiment-driven Quantitative Analysis for Proteomics

Combine multiple complex Scaffold experiments, or directly load Mascot or PEAKS mzIdentML files

Scaffold DIA

Scaffold DIA

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

Scaffold Elements

Scaffold Elements

Scaffold Software Meets Small Molecule LC-MS Analysis

Identify and quantify small molecules using MS1 or MS/MS data

Scaffold PTM

Scaffold PTM

Illuminating the World of Protein Post Translational Modifications

Evaluate modification site assignment confidence using Ascore and Ascore-derived probabilities