Special Help Topics

Collection of help topics that help users optimize their use of Proteome Software products

• Updating MSConvert in Scaffold DIA
• 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
• 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
• Basic Scaffold Workflow
• License Key Tips -- Working with Proteome Software Keys
• TMT Quantiation Settings in Proteome Discover 2.x
• Location of Scaffold, Scaffold Elements and Scaffold PTM Program Settings and Key Files
• Replacing JRE in Scaffold when running Mac OS X
• Replacing Bundled JRE in Proteome Software Products
• Custom Modifications from Mascot Server in Scaffold