Proteome Discoverer Software

Comprehensive, extensible, and intelligent platform

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.

Discover how to transform proteomics mass spectrometry data into insights

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Key benefits

Customize your data analysis	Perform relative quantitation	Extensible 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, MSPepSearch and third-party nodes including Mascot, MSAmanda, Comet, XlinX, Byonic™ from Protein Metrics, Thermo Scientific ProSightPD Software and many more. 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: Tandem Mass Tagging (TMT) with support for MS2 and MS3 based quantification Glycopeptide identification and quantification Phosphopeptide identification and quantification Top-down proteomics Cross-linking Stable Isotope labeled amino acids in cell culture (SILAC) Confidently and efficiently interpret your data with integrated statistical and visualization tools for a faster time to meaningful results.	Build in customization, with the scripting and statistics insights nodes, 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.

Customize your data analysis

Perform relative quantitation

Extensible 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, MSPepSearch and third-party nodes including Mascot, MSAmanda, Comet, XlinX, Byonic™ from Protein Metrics, Thermo Scientific ProSightPD Software and many more. 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:

Tandem Mass Tagging (TMT) with support for MS2 and MS3 based quantification
Glycopeptide identification and quantification
Phosphopeptide identification and quantification
Top-down proteomics
Cross-linking
Stable Isotope labeled amino acids in cell culture (SILAC)

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

Build in customization, with the scripting and statistics insights nodes, 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.

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), proton transfer reaction (PTR), ultra violet photo dissociation (UVPD) and electron transfer dissociation (ETD) in tandem with built-for-purpose search engines.

Customizable data analysis workflows

Simplify data analysis with customizable workflows supporting multiple quantitative methods. Achieve experimental flexibility using TMT, TMTpro, or other isotopic labeling strategies, or opt for label-free quantitation techniques. Map quantitative data to biological information with study management and advanced algorithms for peak selection and peptide quantification, maximizing information extraction from proteomics studies.

Confidently and easily facilitate data comparison, exchange, and verification in compliance with data standards developed by the HUPO Proteomics Standards Initiative (PSI).

Workflow nodes

The workflow system is composed of nodes that can connect in linear or branched pathways. These are highly customizable and pre-defined for common workflows such as TMT, LFQ, PTM identification and cross-linked peptide ID.

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Analysis nodes

Spectra are streamed from the top of the workflow and pass through nodes that perform filtering, peptide ID, quantification, FDR calculation, PTM site localization, bioinformatic analysis, and more.

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Search engine options

The flexible workflows of Proteome Discoverer Software allow for search engines to be used independently, in series, or in parallel to significantly increase the number of peptide and protein identifications.

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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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