Software

Spectronaut is Biognosys’ flagship software and has been the gold standard for DIA proteomics for over a decade. ​

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Spectronaut features two powerful approaches to DIA analysis: a classical library-based approach and directDIA, a proprietary workflow, and top-performing library-free DIA analysis. Additionally, Spectronaut covers all aspects of DIA data analysis, from empirical search space generation through DIA data identification and extraction of quantitative values, followed by post-analysis data visualization and customizable reporting. DIA analysis in Spectronaut was built upon core algorithms using applied artificial intelligence (AI) and machine learning and remains the most AI-augmented DIA software solution available today. ​

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Biognosys is committed to providing cutting-edge solutions to our users via yearly major releases of Spectronaut, launched at the ASMS conference, and interim ad-hoc updates to provide performance enhancements and address any issues quickly.

Spectronaut performs all steps of DIA data analysis, from empirical search space generation through DIA data identification and extraction of quantitative values, followed by post-analysis with extensive data visualization and reporting. ​

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Pulsar, an integrated search engine, allows the user to search DIA data directly in the directDIA workflow without the need to pre-generate spectral libraries. Alternatively, the user can perform library generation using DDA, DIA, or a combination of both, leading to hybrid library generation. ​

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DIA data extraction performed during directDIA analysis or library-based search leads to precursor-level identification and quantification. A variety of settings allows the user to select how protein inference and protein group quantification should be performed for each specific experiment. The software contains a set of default settings that are recommended for the majority of DIA projects.

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Lastly, rich post-analysis functionalities allow for the inspection of DIA spectral matches, quantification, and differential abundance analysis. All results can be exported using customizable reporting options, which enables information archivisation and alternative post-analysis selection.

Pulsar is a search engine integrated into all Biognosys software, including Spectronaut. Pulsar is a versatile search engine performing direct search of both DDA and DIA data from a wide variety of instrument vendors and types. Pulsar can perform searches with a number of predefined or user-defined PTMs and proteases, including unspecific digestion.

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The unique Pulsar capabilities for directly searching DIA data make Spectronaut’s library-free approach a convenient and scalable solution for high-throughput data, including more challenging search spaces with variable PTMs and unspecific digestion.

Spectronaut provides DIA analysis using a classical, library-based approach, as well as directDIA, which is a proprietary Biognosys workflow known for its leading performance in library-free DIA analysis.​

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directDIA is a two-step process that enables direct searching and processing of DIA data without the need to pre-generate a spectral library. In the first step of directDIA, the software performs DIA data deconvolution to pseudo-MS/MS data. This data is then searched by Pulsar, Spectronaut’s integrated search engine, directly against the selected FASTA file. At the end of this step, an on-the-fly search space is generated.​

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In the second step, Spectronaut performs DIA data extraction for each individual DIA run against that search space. Optionally, the user can add extension runs (raw runs or search archives) to further expand the on-the-fly generated search space.​

Yes, library-based DIA analysis is supported in Spectronaut. This workflow requires a spectral library to be generated or imported before setting up the library-based DIA analysis. 

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In the Library perspective of Spectronaut, users can generate a spectral library from DDA and/or DIA raw files (hybrid library) using the Pulsar search engine or from Search Archives. Alternatively, spectral  libraries can be generated using search results from an external search engine or an externally generated spectral library can be imported. When setting up a library-based DIA analysis, different libraries can be assigned to different runs and more than one library can be assigned per run.

Spectronaut features a PTM workflow dedicated to the analysis of post-translational modifications at the site level, including confident localization and differential abundance testing. The novel PTM localization algorithm can work on any variable modification (such as phosphorylation, methylation, acetylation, sulfation, etc.) or combinations of different modifications and does not require specially generated libraries. When the PTM workflow is enabled, Spectronaut provides differential abundance results at the PTM site level including a candidates list and corresponding volcano plot. Additionally, a specialized PTM Site Report is available for export.​

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Finally, Spectronaut offers PTM site-level normalization by protein group quantity from the input samples as well as stoichiometry calculations. 

Yes, by default Spectronaut performs label free quantification (LFQ) applying the MaxLFQ or topN strategy. Using the default settings, precursors are quantified using the area under the curve within the MS2 XIC integration boundaries. ​

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In Spectronaut there are two levels of quantification: minor (peptide) group and major (protein) group. The peptide level will be calculated from the precursors; the protein level will be quantified based on the peptide level.

The Spike-In workflow in Spectronaut allows the user to spike isotopically-labelled reference peptides for the absolute quantification of chosen targets. Note that the pool of spike-in peptides should have the same type of isotopic labelling. Additionally, Spectronaut supports a reverse spike-in workflow in which light peptides are spiked into a heavy-labelled sample.

Spectronaut is Biognosys’ flagship software and has been a gold standard in DIA proteomics for over a decade. Every year, our team releases a new version at the ASMS conference with exciting new workflows and performance improvements. ​

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For the release of Spectronaut 19, we focused on improvements in identification, both on the protein and precursor levels, as well as on improvements in quantification, which is illustrated by higher discovery rates of true candidates in controlled quantitative experiments. ​Additionally, we introduced support for diagonal diaPASEF acquisition and extended support for the PTM and plexDIA analyses.​ Finally, Spectronaut 19 offers improvements aimed at seamless high throughput analysis: faster analysis completion, lower RAM consumption, and expanded command line support.​

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A more detailed description of the new features and improvements in Spectronaut 19 can be found on the Spectronaut 19 launch page.

Spectronaut supports DIA mass spectrometry data collected using instruments from Thermo Scientific, SCIEX, Bruker, and Waters. Specific supported models include: 

Thermo Scientific™ Astral​

Thermo Scientific™ Orbitrap Exploris™ Series​

Thermo Scientific™ Q Exactive™ Series​

Thermo Scientific™ Orbitrap Fusion™ Series​

SCIEX ZenoTOF 7600 System​

SCIEX TripleTOF® Series​

Bruker Impact II​

Bruker timsTOF™, timsTOF™ Pro, and timsTOF™ Ultra​

Waters Xevo® G2-XS qTOF​

Waters Synapt G2-Si

In addition to those listed below, Spectronaut supports a wide variety of DIA data acquisition methods. The minimum requirements are a reversed-phase chromatography with either a linear or nonlinear gradient that spans at least 10-35% acetonitrile. Methods acquiring MS1 and MS2 scans are recommended, but methods acquiring only MS2 scans are also supported (library-based DIA analysis only). The cycle time of the DIA method should aim to sample chromatographic peaks sufficiently. MS1 as well as MS2 scan ranges can be segmented. ​

For more information on setting up a DIA acquisition method, please refer to the user manual.

HRM™​

dia-PASEF®​

SWATH™​

Zeno SWATH​

BoxCar DIA​

SONAR™​

WiSIM-DIA

While we strongly recommend using Pulsar to generate your libraries, Spectronaut also supports generating a library from external search engine results. ​

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To do so, you will need the search result files/folder and the run files from which the search was completed. Spectronaut supports search results from MaxQuant (Cox et al., 2011), Proteome Discoverer™, ProteinPilot™, and Mascot™. In addition to these specific result formats, Spectronaut also supports results in mzIdentML (.MZID) format (containing fragment ion information). Finally, any search results can be reformatted into the Biognosys (BGS) Generic Format, which is defined in the user manual.

Yes, external spectral libraries can be imported into the Library perspective for use in a library-based DIA analysis. Spectronaut accepts Biognosys library format (*.kit) or a compatible spreadsheet as a plain text, separated value format (*.txt, *.csv, *.tsv, *.xls). A table of library columns necessary to achieve the best possible results with Spectronaut can be found in the user manual.

Spectronaut is compatible with Windows and Linux environments. ​

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Chapter 1.3 of the Spectronaut manual contains detailed recommendations for the workstation dedicated to the software installation. ​

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For Windows OS, the user can choose between command line or a convenient general user interface with all the data and results visualizations. Using the Linux version of the software, all workflows and reporting are available via command line. The SNE file generated in Linux OS can be easily open with Windows based Spectronaut Viewer for detailed data visualization and exploration.​

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Spectronaut can be also installed in a Linux or Windows cloud environment. Cloud instances generated for software installation should have similar specs as those ones predefined for local workstations.​

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If you have any further questions about software system compatibility and support, please contact our support team at support@biognosys.com.

Spectronaut software is compatible with Windows and Linux environments, both on local workstations and in the cloud environment.​ For Windows, the minimal versions are Windows 10 or Windows Server 2016. For the Linux-compatible version, Ubuntu 22.04 LTS is supported.​ Installation in the cloud is possible on separate, independent instances but also as a multi-node system engineered for process parallelization. For the latter case, the user should have a multi-seat Spectronaut license (advanced or premium license offering).​ Process parallelization, for high throughput, is also available via the installation of the software on a Linux server. Spectronaut is compatible with configurations on either static or dynamic nodes, depending on the users’ setup.​

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If you have further questions about software system compatibility and support, please contact our support team support@biognosys.com.

Spectronaut licenses come in three different offerings: standard, advanced and premium.​

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Standard allows one software instance installation on Windows or Linux OS. ​

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Advanced licenses comes with five, independent seats. Those seats can be used for local installations on 5 independent workstations or in the cloud environment on 5 independent instances used by different users. Transforming advanced licenses to a floating license model allows parallelization of the analysis with 5 instances. It is also a convenient solution allowing access to the software for a higher number of end users at their own, independent accounts/workstations.​

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Finally, the premium license provides an on-demand number of seats. This model allows all users at a given licensee site access to the software, both as local installations and/or cloud-based installations. The license is issued in the floating model, enabling high-scale parallelized analyses on the users’ infrastructure.

Spectronaut licenses are available in both models: system-bound and floating. By default, standard (1 seat) and advanced (5 seats) licenses are system-bound. However, switching to the floating license model is possible based on user needs. Premium licenses (with a flexible number of seats issued based on user demand) are available as floating licenses, enabling seamless integration into users’ infrastructure for high throughput parallelization. This model is suitable for cloud-based installations as well as multi-node Linux clusters.

We offer various software packages based on your research needs. To receive a quote for Spectronaut, please visit our website here. Click the “Request a Quote” button and fill out the contact form. One of our team members will contact you and provide you with further information.

Tailoring our offerings to meet our customers’ needs, we provide a range of software packages. You can opt for an annual or multi-year license and choose between single or multi-seat options. Spectronaut is compatible with both Windows and Linux, and it’s also cloud-compatible.​
For further information , please visit our website here to request a quote, and one of our team members will reach out to you.

For any of our software, we are happy to offer a 30-day trial license. The trial includes 30-day access to the full version of Spectronaut, access to the video training materials, online consultation session with our software expert, and access to the product support team. ​

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To register for a 30-day free Spectronaut trial, please visit our website here. Click the “Request a Trial” button and fill out the contact form. One of our team members will reach out to you and provide you with further information.

During the free-of-charge 30-day trial, you will be able to work with our demo dataset or your own DIA data to explore workflows and features offered by Spectronaut. ​

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Thanks to the Spectronaut video tutorials available on the Biognosys YouTube channel, you can learn step-by-step how to set up DIA analysis and get a deep overview of the software. ​

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If you have further specific questions during the software trial, our support team will be happy to connect with you for a consultation session to help. Our support team is available at support@biognosys.com.

Spectronaut Viewer allows anyone to open and view results from a Spectronaut analysis (.sne file). However, only Spectronaut active license holders can analyze data in Spectronaut. Our viewer software is free of charge and can be used by an unlimited number of users. Please email order@biognosys.com to have one of our team members reach out to you.​

Spectronaut allows you to save your analysis results in compact and fast-loading files. Because these files can only be opened with our software, we offer Viewer versions of Spectronaut free of charge.​

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The viewer has limited functionality and does not allow analysis of MS data. It can be used to browse saved experiment files, including MS1 and MS2 spectra for identified peptides. Moreover, the user will have an option to review and reintegrate XICs for MS1 and MS2 signals in both the time and ion mobility dimensions. Finally, Viewer has an option to reanalyze after updating some of the settings. Those settings are mainly connected to the quantification method (like settings of normalization or imputation), PTM analysis (e.g. changing localization probability) and differential abundance analysis (e.g. type of statistical test). ​

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Spectronaut Viewer has fully functional post-analysis and report perspectives. The user can readjust cutoffs for the differential abundance analysis and export graphs as well as customized reports with different filtering criteria.​

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By providing this tool, we aim to make data generated with Biognosys software more accessible for review by independent researchers and help to ensure consistent quality of published data in compliance with data submission guidelines of some journals (e.g. MCP). Spectronaut Viewer is also a convenient tool to share results of DIA analysis with collaborators and clients who don’t have access to the full version of the software. Finally, Spectronaut Viewer gives you access to deep visualizations if you run your main software instance in Linux OS without GUI functionalities.​

At Biognosys we aim to support you in using Spectronaut so you will be successful in your proteomics projects with timely, deep and accurate analysis.​ Shall you have any difficulty in applying software to your proteomics project or have a specific question about software algorithm or workflow please reach out to support@biognosys.com. ​

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We provide wide range support for the Biognosys support plan holders via email or via online consultation.

To receive support, Biognosys support plan holders can reach out to support@biognosys.com with a detailed description of their issue or question. We aim to provide timely and streamlined assistance, so we ask that you please include relevant information such as an overview of the type of analysis you are performing, a description of your specific workflows, and an attachment of any associated error logs.

To jumpstart your DIA analyses, we highly recommend watching the short video tutorials available on Biognosys YouTube channel. These videos walk you step-by-step through how to take full advantage of the many intuitive workflows and features available in Spectronaut.​ Additionally, you can find details on many of the software features in the user manual.​

Every Spectronaut release includes exciting new features and improvements in identification and quantification on the precursor and protein group levels. The Spectronaut brochure provides an overview of the main features. For the latest features and improvements in Spectronaut, visit the Spectronaut 19 launch page here.​

On our website you can find multiple resources which will show you different Spectronaut applications and workflow recommendations for a given study question. Click here to browse through the app notes, scientific posters, webinars, publications, and video tutorials. Contact us at support@biognosys.com if you would like to get more information!