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Thermo Scientific Proteome Discoverer Software is the ultimate toolbox for protein research, offering customizable workflows tailored to the complexities of modern proteomics. It simplifies the identification and quantification of proteins in complex biological samples, supporting a wide range of workflows, including peptide and protein identification, post-translational modifications (PTM) analysis, isobaric mass tagging, and label-free quantitation (LFQ). It handles data from diverse acquisition methods, such as data-independent acquisition (DIA), data-dependent acquisition (DDA), and wide window acquisition (WWA), ensuring comprehensive coverage.

Advanced tools like INFERYS™ Rescoring and the CHIMERYS™ intelligent search algorithm by MSAID significantly increase identification rates, protein coverage, and the discovery of unique peptides and PTMs. The software enhances protein quantitation for isobaric mass tags and LFQ, supporting multiple database search algorithms and dissociation techniques. Whether analyzing glycopeptides, top-down proteomics, proteoforms, or MS-based structural biology like chemical cross-linking (XL-MS), Proteome Discoverer Software enables scientists to extract deeper biological insights from their data.

 

Customize your data analysis Perform relative quantitationExtensible workflow tools

Use the node-based workflow editor to customize your data analysis for maximum coverage and confidence. Integrate database search results from multiple search engines such as SEQUEST™ HT, Mascot, MSAmanda, Byonic™ from Protein Metrics, and Thermo Scientific ProSightPD software. Increase confidence in peptide identification and quantification using INFERYS Rescoring and enable a deeper mining of your DIA, DDA, or WWA data using the CHIMERYS intelligent search algorithm.

Measure and report the relative expression levels of isotopically labeled peptides for:

  • TMT SPS MS3
  • Glycopeptide identification and quantification
  • Phosphopeptide identification and quantification
  • Top-down proteomics
  • Cross-linking

Confidently and efficiently interpret your data with integrated statistical and visualization tools for a faster time to meaningful results.

Utilize third-party nodes and build in customization with the scripting node, while maintaining full integration into the Proteome Discoverer software framework to leverage visualization, statistical analysis, and biological interpretation tools to take your analysis to the next level.

Comprehensive tools for proteomic studies

With a wide range of database search options and the ability to combine the output from multiple algorithms, Proteome Discoverer software increases confidence in results and decision making through cross-validation. Augment searches with intelligent INFERYS Rescoring to increase confidence in peptide identification and quantitation. Whether you acquire your data in DIA, DDA, or WWA mode, CHIMERYS intelligent search algorithm helps you dig deeper into your data to substantially increase the number of unique peptide identifications, improve protein coverage, extend quantitation capabilities, and uncover new insights.

Complete sequence coverage and confident identification of post-translational modifications (PTMs) is realized with support for multiple dissociation techniques including collision-induced dissociation (CID), higher-energy collision-induced dissociation (HCD) and electron-transfer dissociation (ETD) in tandem with built-for-purpose search engines.

Customizable data analysis workflows

Automate and simplify data analysis through customizable workflows including full support for multiple quantitative workflows. Enjoy experimental flexibility for quantitation by employing isobaric mass tagging with TMT and TMTpro reagent or other isotopic labeling strategies or utilize label-free quantitation techniques. Map quantitative data to biological information through study management and leverage fast, robust algorithms for peak selection and peptide quantification to extract the maximum possible information from quantitative proteomics studies.

Refine acquisition strategies by generating inclusion and exclusion lists that can be directly imported into instrument methods. Confidently and easily facilitate data comparison, exchange, and verification in compliance with data standards developed by the HUPO Proteomics Standards Initiative (PSI).

Volcano plots and enrichment analysis
Interactive data visualization
Pathway maps
Community-enhanced nodes
Workflow Tools

Manage, automate, process and share proteomics data

The Thermo Scientific Ardia Platform brings together scientific data and results into a centralized location, enabling users to interface intuitively with data, set up automated processing, and easily share results with colleagues and collaborators. Power your data analysis with the platform that brings your data, instruments, and applications together to deliver the future of proteomics workflows.

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Proteome Discoverer 3.1 software

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An intelligent approach to proteomics search.

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