Proteome Discoverer 2.2 Demo

Version Proteome Discoverer 2.2 Demo

Added on:2017-09-19 23:22:47

Description/Changes from last version

This is a fully functional demo version of Proteome Discoverer 2.2 with a license that lasts 60 days.  Afterwards, the software can still be used to view existing result files and perform basic workflow processing.

New Features in Proteome Discoverer 2.2

  • Label free quantification
    • New Minora Feature Detector node
    • Feature Mapper node that performs retention time alignment and matching of features across different runs
    • Support for multi-dimensional data
  • Statistical analysis
    • p-values and adjusted p-values, including a new method for p-value calculation using background protein ratios
    • Pairwise median ratio calculation for LFQ and precursor ion quantification
    • Principal components analysis (PCA)
    • Volcano plots
    • Missing value imputation
  • Mass recalibration
  • KEGG and WikiPathways annotation
  • XlinkX for cross-linked peptide analysis
    • NOTE: 60-day a demo version of XlinkX is included in the third party installer.  To obtain a permanent license for XlinkX, please contact your local sales representative.



  • Processing of large datasets and persistent reports using two-step workflow processing
  • Study management
  • Integration of protein annotations from ProteinCenter
  • Only available as a 64-bit version
  • Peptide and protein FDR, q-values, and PEPs
  • Integration of ptmRS, an algorithm for PTM localization
  • Extensive result export options (text, instrument mass list formats, MGF, mzML, pepXML, protXML, FASTA, etc.)
  • Powerful plotting options with scatter charts, bar and pie charts, histograms, Venn diagrams, Volcano plots, and PCA plots
  • Search automation with Discoverer Daemon (32 and 64-bit versions)
  • Third party nodes include Byonic, Preview (Protein Metrics), ProSightPD (Proteinaceous), MS Amanda, and XlinkX

Installation instructions

This is the 64-bit demo version of Proteome Discoverer 2.2.  The Proteome Discoverer application requires a license.  For this demo version, use the following product key during installation:


Please install the software in the following order:

  1. Microsoft .NET Framework 4.5.1 or higher (if not already installed on your computer)
  2. Proteome Discoverer 2.2
  3. Optionally install the third-party nodes (MS Amanda, Preview, Byonic, ProSightPD, XlinkX). Find details about the third-party nodes in the accompanying instructions for the 'Proteome Discoverer 2.2 Third-Party Nodes' installer in the download section.


Note: Due to technical issues with the portal, the Proteome Discoverer demo software is not available for download.  Please navigate to the Flexera download site ( to find the Proteome Discoverer 2.2 installer.  During installation, please use the product key shown above to activate the 60-day demo.

Hardware/Software requirements


  • 2 GHz processor with 2 GB RAM (8 GB recommended)
  • Video card and monitor capable of 1280 × 1024 resolution (XGA)
  • Screen resolution of 96 dpi
  • 75 GB available on the C: drive
  • NTFS format


  • Microsoft Windows 7 64 Professional (English version) with latest service pack installed
  • Microsoft .NET Framework 4.5.1 or higher
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