Now available: Spectronaut 10 (Orion) with new protein quantification algorithm (Protein Quant 2.0) and Gene Ontology annotation for proteins (Release note)
Please take a look at our General Spectronaut License.
Spectronaut™ software is specifically developed for the analysis of HRM-MS™ (DIA or SWATH™ data sets). HRM, Hyper Reaction Monitoring, is Biognosys’ next generation proteomics technology based on data independent acquisition (DIA) that enables reproducible and accurate quantification of 1000s of proteins in a single instrument run. In combination with the iRT Kit or HRM Calibration Kit Spectronaut™ enables fully automated, fast and accurate signal processing of your DIA or SWATH™ data sets. Contact us for a FREE TRIAL!
Spectronaut™ analyzes a large variety of different DIA methods. Minimal requirements are a reversed phase chromatography with a linear or nonlinear gradient that spans at least 10-35% Acetonitrile. Methods acquiring only MS2 scans are supported as well as methods with both, MS1 and MS2 scans. The cycle time of the DIA method should be in the range of 2-3 seconds depending on the peak width of the chromatography used. MS1 as well as MS2 ranges can be segmented. The MS2 scans should cover at least 500-900 m/z. Gas phase fractionation is supported starting with Spectronaut™ 7 (Nimoy). More specifically Spectronaut™ supports HRM-MS™, WiSIM-DIA, AIF, SWATH™ and SWATH™ 2.0. Multiplexed DIA is not supported.
Minimum: Windows 7 x64, CPU Intel ® Core™ CPU 2.7 GHz (quad core), HDD 200 GB free space, Memory 8 GB, Software .NET 4.5.
Recommended: Windows 7 x64 or higher, CPU Intel Core i7 4770, 3.4 GHz (octa core) or more, HDD 500 GB free space (SSD), Memory 16 GB or more, Software .NET 4.5 or higher.
Current version: 10.0.12817.0
Spectronaut™ Release Overview (Annual Academic Single Named User License)
Spectronaut™ Release Overview (Annual Single System License)
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If you refer to Spectronaut™ algorithms in your research please cite:
Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011;8(5):430-5.
If you refer to the software package please cite:
Bruderer R, Bernhardt OM, Gandhi T, Miladinovic SM, Cheng LY, Messner S, et al. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues. Mol Cell Proteomics. 2015 Feb 27. pii: mcp.M114.044305.
FASTA of iRT peptides for shotgun search
Skyline Schema for exporting Spectronaut compatible libraries - simply add this schema to Skyline’s report list
Spectral library generation using Proteome Discoverer 1.4 (HEK293 cell line sample)
Proteome Discoverer 1.4 Search Files (zip, 1.3 GB) for spectral library generation
Spectral library generation using MaxQuant 1.5 (HEK293 cell line sample)
MaxQuant Search Files (zip, 386 MB) for spectral library generation
HEK293 demo data set
HEK293 demo data set
HEK cell line sample
Window sizes (txt file) - this file is needed only when analyzing the data with software other than Spectronaut™
Visit Science Hub to access all scientific and technical content (publications, videos, application notes, posters and more) related to Biognosys technology, products and services.
Recommended system requirements are: Windows 7 x64 or higher, CPU Intel Core i7 4770, 3.4 GHz (octa core) or more, HDD 500 GB free space (SSD), Memory 16 GB or more, Software .NET 4.5 or higher.Is there a way to calculate the required RAM to analyze and experiment with a spectral library with the size of n precursors and r numbers of DIA runs?
Yes, the required RAM can be calculated using the following formula:
Which mass spectrometric vendors are supported by Spectronaut?
Spectronaut is a vendor independent software. As of Spectronaut 9 the following vendors are supported: ThermoFisher, Sciex and Bruker.My vendor (e.g. Waters) is not supported why is this the case?
Most likely we do not have the vendors API to implement it into the software. If you wish to have your vendors data supported please contact the vendor as well as us at firstname.lastname@example.orgWhich search engines for spectral library generation are supported?
As of Spectronaut 10 search files from MaxQuant, Protein Pilot and Proteome Discoverer are supported to generate spectral libraries directly in the Prepare Perspective of Spectronaut. Further, any search output correctly formatted into the Biognosys Generic Format can be used.My favorite search engine is not supported. What can I do?
Please contact the search engine as well as us at email@example.com and together we can try to get the API of your favorite search engine to support it in future software releases.How does Spectronaut use the iRT peptides?
The iRT peptides are used for retention time and mass calibration in the three pass analysis applied by the software. In the first pass the peptides are used as anchor points to initiate the analysis. Further, the iRT peptides are used in the software for quality control features in the QC Perspective.Is Spectronaut applying normalization and if so what strategy is used?
Per default Spectronaut normalizes the data. The two underlying assumptions are that there are on average no proteins that change in abundance (1) and if there are proteins that are changing then there is the same number of proteins upregulated vs downregulated (2).What does the Q-value stand for and how is it different from the p-Value?
The Q-value is the minimum false discovery rate at which the test may be called significant. As the definition implies it gives a direct measure of the FDR of the identification and quantification.What is the default Q-value cut off used by Spectronaut?
For peptide identification the cut off value is set at Q-value<0.01 for precursor identification. This means that among all true identified precursors there is 1% false positive identifications.
For the statistical testing of differentially abundant proteins the Q-value is set at Q-value<0.05.How is the Q-value for peptide identification calculated?
In total more than 12 different measurements are used to calculate the Q-value for a given peptide. Among the values factoring into the equation are iRT accuracy, relative fragment ion intensities many more.How are the differential abundant candidates in the Post Analysis Perspective calculated?
To determine the proteins differentially abundant between different conditions Spectronaut is performing a one sample t-test on the log ratios of all features between all conditions. For the protein quantities the average precursor intensities are used per default.I do not like the default settings where can I change them?
The Biognosys factory settings or also called default settings have proven to be suitable for the majority of the experimental set ups. Yet, sometimes individual settings are necessary. To perform data analysis using user defined settings there are two options available. Option 1: the settings are modified in the Review Perspective when setting up the experiment. Option 2: In the Settings Perspective the settings are modified and stored in a separate settings schema.I want to subject the data generated in Spectronaut to third party analysis tools how can I do this?
The Report Perspective is design in a way that all accessible information can be exported. For certain downstream analysis tools a reporting schema can be created based on the information needed. If you need help establishing a schema do not hesitate to contact us at firstname.lastname@example.orgCan I use other peptides than the iRT peptides for QC monitoring?
Yes, in the Prepare Perspective the library can be used to generate a pool of peptides suitable for QC. This additional panel can be used in the QC Perspective.
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