Product Documentation
Frequently Asked Questions
- Recommended FDR Settings for Loading Spectrum Mill Data into Scaffold
- Reference Libraries Used in Scaffold DIA
- DIA Proteomic Searches and FASTA File Size (Number of Entries)
- Processing Vendor Raw Data with ProteoWizard
- Scaffold Products and High Resolution Displays
- Changing Temp Space For Each Scaffold Batch Run
Product Documentation
- Proteome Software File Extensions
- License Key Nomenclature
- Scaffold DIA File Compatibility Matrix
- Getting Started with Scaffold: A Primer for Viewer Users
- Scaffold File Compatibility Matrix
- Elements File Compatibility Matrix
Special Help Topics
- UniProt FASTA References
- Moving Proteome Software Products from One Computer to Another
- Thermo Windowing Schemes for DIA Proteomics
- Chromatogram Libraries Improve Peptide Detection and Quantification by DIA Mass Spectrometry
- Searching FASTAs with Scaffold DIA, Resource-Intensive Process
- Isobaric Tagging (TMT, iTRAQ) and mzIdentML/MGF Files
White Papers
- Scaffold DIA Search Performance Benchmark
- Designing DIA Mass Spectrometry Methods
- The Permutation Test
- Terminology Comparison: Legacy Scaffold and Scaffold 4
- Scaffold Precursor Intensity Quantitation
- Protein Grouping and Clustering in Scaffold
PS Product Citations
Introductory Material
Presentations
- Introduction to DIA: Data-Independent Analysis
- A Complete Framework for Metabolomics
- Scaffold: The New Quantify View
- Analysis of GeLCMS Data in Scaffold
- Improving Quantitation with Scaffold PTM
- X! Tandem Explained