Documentation
Getting Started with Scaffold Software
- Data Independent Acquisition Proteomics Resources - DIA Tips
- Designing DIA Mass Spectrometry Methods
- Getting Started with Scaffold DIA: Part 1
- Getting Started with Scaffold DIA: Part 2
- Introduction to Metabolomics
- Introduction to Proteomics
Supported Data Formats
- Configure Mascot Server 3.0 to Write Results in DAT (dat28) Format
- Configuring FragPipe for Scaffold
- Scaffold Software Supported Data Formats
- Loading PEAKS Data into Scaffold
- Configuring Proteome Discoverer 2.2 and forward for Compatibility with Scaffold
- Configuring Proteome Discoverer 2.0-2.1 for Compatibility with Scaffold
Frequently Asked Questions
- Custom Modifications in Scaffold Software
- Skip Running msConvert in Scaffold DIA (eg, To Run mzML Files)
- Removed Fisher's Exact Test From Scaffold 5
- DIA: Peptide- vs Spectrum-centric searching and PTMs
- Scaffold Software Stuck in Viewer Mode
- Is Scaffold Software compatible with M1 and M2 Apple computers?
Using Scaffold Software
- Scaffold DDA Batch Processing using the Command Line Interface (CLI)
- Custom Digestion Enzymes Configuration in Scaffold DIA Workflows
- Commandline Arguments for Running msConvert CLI
- Connecting to your Mascot Server from Scaffold
- Transitioning from Scaffold LFQ to Scaffold DDA Label-free Quant
- JRE Licensing and Scaffold Software
Presentations, Papers and Posters
- Presentations from Virtual Brunch 2021
- Presentations from Virtual Brunch 2020
- Chromatogram Libraries Improve Peptide Detection and Quantification by DIA Mass Spectrometry
- EncyclopeDIA: Library Searching for Data-Independent Acquisition
- Introduction to DIA: Data-Independent Analysis
- Proteome Software Conference Posters
Articles Citing Scaffold
Company
Contacting Us
Release Note Archive
- Scaffold Software and Log4j
- Scaffold Quant Release Notes
- Scaffold LFQ Release Notes
- Scaffold DIA Release Notes
- Scaffold Elements Release Notes
- Scaffold perSPECtives Release Notes