Proteomics Software | DIA Proteomics | Discovery Proteomics
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Spectronaut™

The gold standard for DIA proteomics analysis

Thanks to deep-learning augmented peptide identification, you can now find more precursors and proteins in your samples than ever before. We have further broadened our support for the latest mass spectrometry data acquisition technologies, and provide new ways to quickly and thoroughly analyze data.

      Spectronaut™ is a commercial software package aimed at analyzing data-independent acquisition (DIA) proteomics experiments. Spectronaut™ can quantitatively profile 100s to several 1,000s of proteins in one experiment. Large experiments with several conditions and replicates consisting of up to 10,000s of LC-MS runs can be analyzed.

      Features:

      1. Vendor Independent
      2. Usability
      3. Complete Workflow
      4. Performance and Scalability
      5. Versatility and Flexibility

       

      Check out what’s new in Spectronaut™ 15.

      Supported Instruments

       

      • Thermo Scientific™ Orbitrap Exploris™ 480
      • Thermo Scientific™ Q Exactive™ Series
      • Thermo Scientific™ Orbitrap Fusion™ Series
      • SCIEX TripleTOF® Series
      • Bruker Impact II
      • Bruker timsTOF™ and timsTOF™ Pro*
      • Waters Xevo® G2-XS
      Supported Methods

       

      • HRM™
      • BoxCar DIA
      • WiSIM-DIA
      • SWATH™
      • SWATH™ 2.0
      • SONAR™
      • dia-PASEF®

       

      Methods should acquire MS1 and MS2 or MS2 only scans. The cycle time of the method should be in the range of 1-3 seconds depending on your average peak width. Fractionation, including gas-phase fractionation, is supported.

      Recommended System Requirements*

       

      • Windows 10 x64 / Windows Server 2016
      • Intel or AMD CPU with 4 cores or more
      • 2 TB of free hard drive space or more (2x data set size)
      • 16 GB of memory or more (1 precursor in 1 run amounts to ~0.5 KB of RAM)

       

      *For a typical experiment of 200 runs with a 100k precursor library

      If you are interested in ordering one of our softwares, please submit a request form or contact us. Our team will review your inquiry and get back to you within 5 working days.

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      Launch Pages

      Spectronaut™ 15: Expand Biological Insights with DIA Proteomics

      Spectronaut 15 comes with many novel and enhanced features for the most complete and versatile quantitative proteomics software.


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      Brochures & Flyers

      Spectronaut™ Brochure – Take your DIA data to the next level

      The brochure provides you with an overview of the key features and benefits which make Spectronaut the gold standard software for DIA proteomics analysis. The brochure elaborates o [...]


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      Software Tutorials

      Spectronaut™ 15 – A new way to visualize your DIA data

      Fabia Simona from our Product Support Team walks you through the most significant improvements to the user interface in Spectronaut 15. Gain even more biological insight from your [...]


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      User Resources

      Spectronaut™ Manual

      The Spectronaut manual is designed to support users and leverage their DIA data analysis experience. It covers software features and analysis workflows and guides the user through [...]


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      User Resources

      Spectronaut™ Demo Data Set

      includes: Six run files, FASTA file, Spectral library file, Condition setup file, Gene Ontology Annotation file, Experiment file (sne file)


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      User Resources

      Spectronaut™ Further User Resources

      includes: FASTA for iRT peptides Skyline Schema for exporting Spectronaut compatible libraries


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      Software Tutorials

      Spectronaut™ 15 – A new way to visualize your DIA data

      Fabia Simona from our Product Support Team walks you through the most significant improvements to the user interface in Spectronaut 15. Gain even more biological insight from your [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to perform PTM analysis

      Spectronaut features extensive support for PTM studies including site-based PTM localization probabilities, quantification, regulation analysis, and reporting.


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      Software Tutorials

      Spectronaut™ Tutorial – How to process your data more efficiently with Pipeline Mode and SNE Combine

      Spectronaut offers powerful features to handle large datasets. Maximilian Helf from our R&D department shows you how to queue up analysis jobs in pipeline mode and introduces S [...]


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      Seminar Recordings

      Reshaping DIA based Proteomics with Spectronaut™ 14 – ASMS 2020 Reboot

      In this Spectronaut 14 launch seminar at ASMS 2020 Reboot, we summarize the most ground-breaking new features of this major release of Spectronaut: a) directDIA 2.0, a major improv [...]


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      Seminar Recordings

      Spectronaut™ User Seminar I – ASMS 2020 Reboot

      This seminar at ASMS 2020 Reboot, had two exceptional speaker: Prof. Jesper Olsen and Prof. Florian Meier. First, Prof. Olsen shows, among other great results, how the combination [...]


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      Seminar Recordings

      Spectronaut™ User Seminar II – ASMS 2020 Reboot

      This seminar at ASMS 2020 Reboot had the participation of two outstanding Spectronaut advocates: Prof. Birgit Schilling and Prof. Yansheng Liu. First, Prof. Schilling shows how she [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to jump-start your DIA analysis

      Fabia Simona from our Product Support team shows you how to set up a DIA analysis in Spectronaut and gives valuable tips on setting up the software for optimal performance on you c [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to perform directDIA™ in two steps

      One of the most popular features of Spectronaut is directDIA, allowing you to run DIA analysis without additional files for library generation. In this video tutorial, Fabia Simona [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to get the most out of your ion mobility data with Spectronaut™

      Spectronaut supports Ion Mobility Technologies from different vendors. Monika Puchalska from our Product Support team demonstrates how to take advantage of Thermo’s FAIMS or [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to visually inspect peptide-spectrum matches in Spectronaut™ & SpectroMine™

      Getting detailed information on peptide-spectrum matches (PSMs) is important to verify identifications and access to PSM information is required for data submission to many journal [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to make a spectral library for a labeled DIA experiment using Pulsar™

      SILAC experiments as well as the use of isotopically labeled reference peptides require specific changes to your experiment setup in Spectronaut. Tejas Gandhi from our R&D team [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to run Spectronaut™ from the command line

      Spectronaut command line enables you to run analyses without manual interaction, for instance from scripts. Maximilian Helf from our R&D team shows you how to use Spectronaut c [...]


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      Software Tutorials

      Spectronaut™ Tutorial – How to speed up your Spectronaut™ analysis with HTRMS conversion

      Spectronaut uses the HTRMS file format for high performance data analysis. Oliver Bernhard from our R&D team shows you how to save up to 60% analysis time by converting your fi [...]


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      Publications

      Surpassing 10 000 Identified and Quantified Proteins in a Single Run by Optimizing Current LC-MS Instrumentation and Data Analysis Strategy

      Muntel J et al. Molecular Omics. In this study we showed how improvements in chromatography and data analysis can push the proteome coverage in human tiss [...]


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      Publications

      Systematic Comparison of Strategies for the Enrichment of Lysosomes by Data Independent Acquisition

      Singh J et al. Journal of Proteome Research. The lysosome is a critical cell compartment dedicated to the recycling of macromolecules and organelles, and [...]


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      Publications

      Isoform‐resolved Correlation Analysis between mRNA Abundance Regulation and Protein Level Degradation

      Salovska B et al. Molecular Systems Biology. In a collaboration between Prof. Liu’s group at Yale University and Biognosys, we established a combined DI [...]


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      Publications

      Revealing Dynamic Protein Acetylation across Subcellular Compartments

      Baeza J et al. Journal of Proteome Research. In this study, the Biognosys’ R&D team, in collaboration with researchers of the University of Wisconsi [...]


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      Publications

      Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

      Bekker-Jensen DB et al. Nature Communications. Protein phosphorylation is a predominant post-translational modification that dynamically regulates protein [...]


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      Publications

      Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition

      Huang T et al. Molecular & Cellular Proteomics. In this publication, we report a novel statistical procedure that takes advantage of the two independe [...]


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      Publications

      Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows with Fixed Instrument Time

      Muntel J et al. Journal of Proteome Research. Here we compare the performance of the two most popular quantitative workflows employed in discovery proteom [...]


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      Publications

      Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

      Bruderer R et al. MCP. In this work, Biognosys and collaborators compared proteome coverage and quantification performance of the emerging DIA/SWATH metho [...]


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