Preface - ProSightPD - Proteome Discoverer Software - ProSightPD 4.4 User Guide - Preface - ProSightPD - ProSightPD - Proteome Discoverer Software - Proteome Discoverer Software

ProSightPD 4.4 User Guide
Product Tree
Desktop Software > Proteome Discoverer Software > ProSightPD
Ardia Platform > Software > Proteome Discoverer Software > ProSightPD
Ardia Platform > Software > Proteome Discoverer Software
Desktop Software > Proteome Discoverer Software
Document Type
User Guide
Software version
4.4
  • ProSightPD User Guide
  • Preface
  • Access documentation
  • About this guide
  • Software installation and activation
  • Download the software
  • Activate the software license
  • Enter the product ID and the activation code
  • Complete license activation on a computer that is connected to the Internet
  • Special notices
  • Contact us
  • Overview
  • Introduction to ProSightPD
  • Introduction to top-down proteomics
  • ProSightPD workflow overview
  • Working with example data
  • ProSightPD database search algorithms
  • Annotated proteoform search
  • Subsequence search
  • Delta M Mode searches
  • Label-free quantitation and sliding window deconvolution
  • Creating and maintaining databases
  • Top-down databases in ProSightPD
  • Create a database in ProSightPD
  • Download a ready-to-use database
  • (Optional) Edit isoforms in ProSight Annotator
  • (Optional) Expand Isoforms to Proteoforms
  • Add an available feature to the included feature set
  • Create a ProSightPD database from an existing FASTA database in Proteome Discoverer
  • Export a FASTA database from Proteome Discoverer
  • Create a database from a FASTA format file
  • Change the isoform mass threshold
  • Building a top-down database from a bottom-up result file
  • Build a database from a single sequence
  • Delete databases from the Database Manager
  • Working with studies
  • Studies
  • Create a study
  • Processing workflows, consensus workflows, and analyses
  • Configure a workflow
  • Use or edit an analysis template
  • Use or edit a workflow after creating the study
  • Replace a node in a workflow
  • Configure application specific worflows
  • Label-free quantitation
  • Isotope labeling
  • Perform Annotated Proteoform searches in the processing workflow
  • Add an Annotated Proteoform search in the processing workflow
  • Perform a Subsequence search in the processing workflow
  • Add a Subsequence search in the processing workflow
  • Perform Single Proteoform searches in the processing workflow
  • Perform single proteoform searches in the processing workflow
  • Working with results
  • The results report
  • Proteins page
  • Isoforms page
  • Proteoforms page
  • PrSMs page
  • MS/MS Spectrum Info page
  • Work with the MS/MS Spectrum Info page
  • Input Files page
  • Specialized Traces page
  • Quantitative results in ProSightPD
  • Feature Group page
  • Consensus Feature Group page
  • Quantitative results columns in the Proteoforms page
  • Visualizing top-down results
  • Use ProSight Lite
  • Use TDViewer
  • Install the TDViewer
  • Generate a compatible result file report
  • Use TDValidator Lite
  • Filter results
  • Visualize results with charts and graphs
  • Histograms
  • Abundances
  • Volcano Plot
  • Scatter Plot
  • Chromatogram Traces view
  • Workflow templates and analysis templates
  • ProSightPD nodes
  • Server Utilities node
  • FASTA Exporter node
  • Feature Detector nodes
  • Med Res. Feature Detector
  • Hi Res. Feature Detector
  • Search nodes
  • Annotated Proteoform Search node
  • Advanced parameters of the Annotated Proteoform search
  • Single Proteoform Search node
  • Subsequence Search node
  • Advanced parameters of the Subsequence search
  • Tag to Annotated Proteoform Search node
  • Tag to Subsequence Search
  • cRAWler nodes
  • PTCR cRAWler node
  • High/High cRAWler node
  • Med/High cRAWler node
  • ProSightPD Consensus nodes
  • PrSM Grouper node
  • Protein Grouper node
  • FDR node
  • Proteoform Validator node
  • Proteoform and Protein Filter node
  • Feature Mapper node
  • Quantifier node
  • PFR Annotator node
  • Interpreting results
  • P-Score
  • C-Score
  • Expectation Value (E-Value)
  • Legal notices
  • Copyright and trademarks
  • Revision history

This guide describes how to use the Thermo ProSightPD™ 4.4 nodes in the Proteome Discoverer™ 3.2 application to perform top-down proteomics data analysis.

  • Access documentation
  • About this guide
  • Software installation and activation
  • Download the software
  • Activate the software license
  • Special notices
  • Contact us
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