Star-quality proteomics software.

Spectronaut™ Pulsar is specifically developed for the analysis of data independent acquisition (DIA) measurements. Spectronaut™ Pulsar analyzes the acquired signals with a spectral-library-free workflow, directDIA™, or with a targeted analysis of the data using spectral libraries (Hyper Reaction Monitoring  – HRM™). It features Pulsar, Biognosys’ proprietary database search engine, which supports both workflows and eliminates the need for external search engines.

• Unmatched proteome coverage: ideal for discovery proteomics applications
• Fast analysis of large data sets with minimal bioinformatics resources
• High confidence in your data with complete workflow quality controls
• Simple, easy to use and instrument-vendor independent
• Supports the spectral-library-free workflow and targeted analysis of DIA data using spectral libraries

Click for more information about Spectronaut™ Pulsar

The story of discovery proteomics.

Discovery proteomics aims to understand global proteome dynamics, for instance in cells, tissue or an organism. The key to gain a comprehensive picture of the biology lies in the quantitative precision, reproducibility and the unbiased nature of analysis at the highest possible protein coverage.

Modern discovery proteomics relies mainly on bottom-up mass spectrometry methods where peptides from corresponding proteins are detected with high-resolution LC-MS/MS instruments and then identified and quantified using state-of-the-art software solutions.

An important part of the high-resolution LC-MS/MS instruments is electrospray ionization (ESI). ESI is an ionization technique for large biomolecules that produces ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. The ESI was developed by John Fenn who was awarded the Nobel Prize in Chemistry in 2002.

Until today, data dependent acquisition based proteomics (DDA) is the most widely used discovery proteomics technique. A major limitation of DDA based proteomics, however, is the semi-stochastic peptide selection for its identification. Therefore, the same peptides will not be identified reproducibly even when analyzing technical replicates. Despite the possibility of performing MS1 alignment, this results in a high number of missing values in the data matrix, which causes problems in the statistical analysis and an incomplete biological picture.

Recently, data independent acquisition methods (DIA) have emerged as an alternative, where in a single measurement, all detectable peptides can be quantified with high sensitivity, quantitative precision and reproducibility. DIA thus features higher data completeness (gap-free raw data) and lower technical CVs across the full range of detectable proteins compared to the DDA workflow.

However, for best performance, a spectral library typically generated from DDA runs is necessary for targeted data analysis of DIA. This increases the instrument run time and especially in small experiments presents a significant cost overhead. With the introduction of directDIA™, a spectral-library free data-independent acquisition (DIA) workflow, proteomics researchers now have a workflow with the benefits of the quantitative precision and the reproducibility of DIA combined with the operational simplicity of DDA.

Implemented in the new Spectronaut™ Pulsar analysis software, directDIA™ is now easily accessible to every proteomics researcher. Spectronaut™ Pulsar allows the user to perform directDIA™, which enables reproducible and precise quantification of thousands of proteins in a single measurement – without the need for DDA-based spectral libraries.

Powerful as DIA. Easy as DDA.

directDIA™ and HRM™ workflows.

Biognosys' solutions support every step in the directDIA™ and HRM™ workflows.


The new directDIA™ workflow and Spectronaut™ Pulsar analysis software enable reproducible and precise quantification of thousands of proteins in a single measurement without the need for DDA-based spectral libraries.


HRM™ is a DIA-based workflow where a spectral library is needed as a template for peptide identification during data analysis. HRM™ is optimized for maximum depth of analysis and highest number of identified and quantified proteins.

Free trial!

If you’re interested in learning more about Spectronaut™ Pulsar or to get a free trial, don’t hesitate to contact us at We would be pleased to schedule a meeting and support you in implementing next-generation proteomics solutions in your lab.

FAQ – frequently asked questions.

What is the difference between directDIA™ and HRM™ workflows?
directDIA™ and HRM™ are data independent acquisition (DIA) based workflows that provide comprehensive proteome coverage by multiplexing thousands of proteins. directDIA™ is a simple workflow that doesn’t require additional runs for spectral library generation. In HRM™, additional DDA or DIA runs are needed for spectral-library generation to produce the highest possible number of identified and quantified peptides and proteins.

What is Pulsar?
Pulsar is Biognosys’ proprietary database search engine, which is integrated into Spectronaut™. This search engine implements a dynamic PSM-stratification strategy to maximize identifications in large data sets and to control FDR on PSM subsets such as modified peptides.

Can I use external database search engines with Spectronaut™ Pulsar?
Yes, Spectronaut™ Pulsar supports external search engines MaxQuant, Mascot, Proteome Discoverer and ProteinPilot in addition to Pulsar for HRM™ experiments. However, directDIA™ workflow is only possible with the use of integrated Pulsar search engine.


Learn more about Spectronaut™ Pulsar and directDIA™ by joining our live webinar.
When: Monday, June 26th 2017 at 4:00pm CET (10:00am EST)

Lukas Reiter, Chief Technology Officer
Oliver Bernhardt, Senior Scientist Bioinformatics
Stephan van Sint Fiet, Chief Commercial Officer

Please contact us at to get a video recording of the Spectronaut™ Pulsar webinar.

Register to the webinar here!

The new era in discovery proteomics.

You will soon be able to achieve DIA-class performance, without generating a spectral library. Now made possible with the directDIA™ workflow developed by Biognosys.

DIA performance, DDA simplicity.
Available 2 June 2017.

Spectral-library free data-independent acquisition (DIA)

– by Biognosys.

Thank you for taking our quiz!

We are happy to announce that many visitors took our proteomics quiz. Among the ones who got all five questions right, we drew one lucky winner who is announced below. The correct answers:
Which biomolecules are detected using bottom-up mass spectrometry proteomics?
Correct answer: Peptides
What are the main discovery proteomics workflows called?
Correct answer: DDA and DIA
Large-scale analysis of peptides would not be possible without electrospray ionization (ESI). Who was awarded the Nobel Prize for his research concerning this technique?
Correct answer: John Fenn
What are the key advantages of DIA over DDA?
Correct answer: Higher data completeness and Lower CVs
Which part of the standard DIA workflow will be redundant with the new directDIA™?
Correct answer: DDA runs for spectral-library generation

And the lucky winner of the Apple Watch is

Hua Liao, Takeda, USA

CONGRATULATIONS! Your Apple Watch is on its way!

Take our quiz and compete to win an Apple Watch!

Are you keeping track of what's going on in the world of proteomics? Then you should have a go at our quiz. Get all five questions right and you'll have a chance to become the lucky winner of an Apple Watch. Just click in your answers and submit your contact information below. Good luck!

Note: The competition closes on 1 June. The winner will be announced here on on 2 June.
Which biomolecules are detected using bottom-up mass spectrometry proteomics?
What are the main discovery proteomics workflows called?
Large-scale analysis of peptides would not be possible without electrospray ionization (ESI). Who was awarded the Nobel Prize for his research concerning this technique?
What are the key advantages of DIA over DDA?
Which part of the standard DIA workflow will be redundant with the new directDIA™?
Thank you!
You are now in the competition! The winner and the correct answers will be announced here on on 2 June.
Oops! Something went wrong when submitting the form. Please try again!

Meet us at ASMS 2017 to network with us and to learn about the latest innovations in next-generation proteomics.

1. Biognosys user meeting

When: Sunday 4 June, 1–4pm
Where: Westin Hotel Indianapolis, room Grand 3


From DDA to DIA: A comparative approach.
Christian D Kelstrup, University of Copenhagen
Pulsar: A very fast search engine for spectral-library generation and directDIA™ analysis.
Lynn Verbeke, Biognosys
Absolute quantification of the human plasma proteome by using stable-isotope-standard peptides in different data-independent-acquisition analysis workflows.
Florian Marty, Biognosys

2. Biognosys breakfast seminar

When: Tuesday 6 June, 7am
Where: Indiana Convention Center, room 130


Evolution of DIA at Biognosys
Lukas Reiter, Biognosys
Spectronaut™ Pulsar – introducing the new era in proteomics
Florian Marty, Biognosys

3. Biognosys presentations

When: Wednesday 7 June, 9:30am
Where: Indiana Convention Center, Hall D level 1
Section: Informatics: Data-independent acquisition: Innovative methods and applications


Spectral-library-free DIA (DDA-free DIA) algorithm applied to data generated on a novel fast-scanning Orbitrap instrument
Lukas Reiter, Biognosys

4. Biognosys posters

Where: Indiana Convention Center


Reproducible single-shot plasma proteome rofiling with high throughput capabilities on a robust capillary flow setup (MP040)
Roland Bruderer, Biognosys
Pulsar: A search engine integrated into Spectronaut using Dynamic PSM Stratification (MP330)
Lynn Verbeke, Biognosys
Having a free lunch: A combined DIA+DDA approach towards spectral-library generation for DIA analysis using Spectronaut (WP080)
Tejas Gandhi, Biognosys
Advances in targeted analysis of Centroided DIA/SWATH with Spectronaut. Equal performance for up to ten-fold lower storage demand (WP313)
Oliver Bernhardt, Biognosys

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