Spectronaut: The Deepest Proteome Coverage Available

Spectronaut® 16: The Deepest Proteome Coverage Available

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Spectronaut® 16 brings users the ability to identify and quantify more from their DIA data than ever before. With an improved directDIA workflow, new deep learning scores, and an enhanced user experience, DIA data has never been this meaningful.

“With Spectronaut 16, our users can achieve deeper proteome coverage than with any other solution on the market, while benefiting from a seamless user experience.”


Lukas Reiter, Ph.D., CTO of Biognosys

Feature Overview

  • Record identifications: Identify a record number of precursors and proteins with a completely new machine learning framework.


  • Deep learning augmented: Novel applications of deep learning improve both spectrum- and peptide-centric workflows


  • Improved Pulsar search engine: Significantly faster spectrum-centric searches with more IDs using Pulsar.


  • Improved directDIA workflow: With our new one-step workflow, Hybrid directDIA has never been easier.


  • Enhanced user experience: The best DIA user experience got even better with new visualizations and reporting options.


More Identifications than Ever Before

Spectronaut 16 offers an unprecedented boost in identifications. Here we show a comparison with Spectronaut 15.


These improvements apply to both library-based and library-free workflows. Identification numbers are also consistently higher across all instrument vendors, ensuring significant improvements for all Spectronaut users.


To guarantee that you can trust your Spectronaut data, the software’s run-wise protein FDR control makes sure that your results are accurate every time, without compromising on the number of identifications.

Unmatched High-throughput DIA

Spectronaut 16 consistently outperforms other solutions when analyzing high-throughput DIA data.


When testing Spectronaut 16 against exemplary short-gradient DIA data1,2 our results demonstrate that Spectronaut 16 identifies more precursors and more protein groups than other solutions on the market. Comparable results were observed for FAIMS data.

Get the Most out of Your Plasma Data

Blood plasma is an important cornerstone in detecting and monitoring the progression of many diseases.


With Spectronaut 16, analyzing plasma data is more accurate than before.


Spectronaut 16 is not only able to identify more protein groups in plasma than Spectronaut 15, but also recovers significantly more true candidates when measuring mixed proteome samples spiked in different amounts (Human depleted Plasma 1:1, E. coli 1:0.4, S. cerevisiae 1:1.3).

How to Perform directDIA with Library Enrichment in Spectronaut

With Spectronaut 16 it is easier than ever to work with enriched directDIA data. This powerful workflow is now easily accessible with the click of a button to make your Hybrid directDIA analysis the smoothest yet.


In this tutorial, Monika Puchalska from our Product Support team demonstrates how easy it is to set up your enriched directDIA analysis in Spectronaut.


In addition, Monika provides an overview of the new visualization options in Spectronaut 16 that help you get insights from your DIA analysis results even faster.

More about Spectronaut 16

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