Frequently Asked Questions
A section to quickly get FAQs about Proteome Software products
- Transitioning from Scaffold LFQ to Scaffold DDA Label-free Quant
- Installing Scaffold Software when installations are blocked by your operating system
- Scaffold t-test
- Searching with MSFragger and X! Tandem in Scaffold 5
- Why use reviewed FASTA entries for generating Prosit libraries
- Free Scaffold Viewer
- Running More Than One Copy of Scaffold
- Windows Smart Screen and Installing Scaffold
- Scaffold DIA Error: Percolator Exited with Non-zero Status
- How to Completely Remove Scaffold from Your System
- Upgrading Scaffold, Workstation Hardware, or your Operating System
- Scaffold Scoring Models and Filtered Data
- Recommended FDR Settings for Loading Spectrum Mill Data into Scaffold
- UniProt FASTA References
- Reference Libraries Used in Scaffold DIA
- Moving Scaffold Software from One Computer to Another
- DIA Proteomic Searches and FASTA File Size (Number of Entries)
- Processing Vendor Raw Data with ProteoWizard
- Scaffold DIA FASTA Searches Do Not Support Multiple Variable Modifications
- Scaffold DIA Search Performance Benchmark
- Scaffold Products and High Resolution Displays
- Changing Temp Space For Each Scaffold Instance
- Gene Ontology: Custom Annotations in Scaffold
- Scaffold "Versioning Problem" Error Message
- Running Multiple Instances of Scaffold on One Computer
- Spectrum Count Normalization in Scaffold
- The Benjamini-Hochberg Correction
- The Permutation Test
- Scaffold PTM Views and Displays
- Views and Displays in Scaffold Q+S