Product Documentation
Frequently Asked Questions
- Processing Vendor Raw Data with ProteoWizard
- Scaffold Products and High Resolution Displays
- Changing Temp Space For Each Scaffold Batch Run
- Scaffold "Versioning Problem" Error Message
- Proteome Software Resellers
- Spectrum Count Normalization in Scaffold
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
- Isobaric Tagging (TMT, iTRAQ) and mzIdentML/MGF Files
- Accessing Wiki Pathway information from Scaffold
- Scaffold DIA FASTA Searches Do Not Support Multiple Variable Modifications
- Running Multiple Instances of Scaffold on One Computer
- The Benjamini-Hochberg Correction
- Use of the Chromatographic System Feature in Elements
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