Spectronaut® 17: A Groundbreaking Increase in Identifications - Biognosys

Spectronaut® 17: A Groundbreaking Increase in Identifications

Seminar Recordings

The application of DIA to proteomics has made some extraordinary improvements over the past decade. From the start, Biognosys’ Spectronaut® software has been the gold standard for DIA analysis with numerous improvements throughout the years. None have been as significant as the changes Spectronaut 17 introduces. With the addition of directDIA+, Spectronaut goes beyond what any other DIA analysis software has done before.


During this seminar, you will learn what makes Spectronaut 17 our most groundbreaking release yet. First, Lukas Reiter, Biognosys’ CTO, will introduce directDIA+, what it means for your DIA analysis, and how you can apply it. Then, Jesper Olsen (University of Copenhagen) will present how this new way of processing DIA data enables his team to go significantly deeper into the proteome without the need for a library.

Spectronaut 17 and directDIA+ establish library-free analysis as the de facto standard

Spectronaut 17 for Deep Proteome and Phosphoproteome Analysis

Lukas Reiter (Biognosys)

For many years using a project-specific experimental library was a prerequisite to take full advantage of DIA. However, generating project-specific libraries is a major complication of the workflow. Hence, over the years library-free analysis, as implemented with directDIA in Spectronaut, has become more and more popular. With Spectronaut 17 and directDIA+ we introduce improved deep learning models that make library-free analysis the de factor standard.

Jesper V. Olsen (University of Copenhagen)

In this presentation, I will show a benchmark of Spectronaut v. 17 (SN17) against the previous SN16 for DIA analysis of human cell line and species proteome mixtures using the spectral library free approach. For both single-shot LC-MS/MS and offline high-pH C18 reversed phase fractionated tryptic digests, the new directDIA+ in SN17 provides significantly more peptide and protein identifications while preserving the quantitative accuracy. Moreover, specifically for analysis of phosphoproteomics datasets, SN17 effectively increase the number of phosphopeptide identified by ~25% compared to SN16 and DIA-NN, both with and without the use of deep spectral phosphopeptide libraries.

Short Bio Lukas Reiter:

Lukas graduated from ETH Zurich in molecular biology. For his PhD, he joined the groups of geneticist Michael Hengartner and proteomics pioneer Ruedi Aebersold and received his degree in 2009 from the University of Zurich. After that Lukas joined Biognosys in 2010 as one if its first employees. As CTO, he oversees research as well as product and workflow development at Biognosys. Lukas is fascinated by proteomics technology and the idea of making it available to everybody who needs to know about proteins.

Short Bio Jesper V. Olsen

Jesper Olsen studied analytical chemistry at the University of Southern Denmark in the laboratory of Roman Zubarev. After this, he worked for two years at MDS Proteomics as a staff scientist before joining the laboratory of Matthias Mann as PhD student. He spent 4 years as a post-doctoral fellow at the Max Planck Institute for Biochemistry in Munich. In 2009, Jesper was recruited to head a research group at the newly established Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen (UCPH). In 2012, he was promoted to vice director of CPR and in 2014 full professor at UCPH.

Jesper has made seminal contributions to the field of proteomics and high-resolution mass spectrometry and pioneering quantitative phosphoproteomics technology and its application to study cell-signaling networks to answer outstanding questions in biology. His group is developing proteomics technology and their work on offline peptide chromatographic fractionation in combination with fast online LC-MS/MS has enabled a comprehensive analysis of human proteomes. Most recently, his group has worked on the combination of FAIMS and DIA on the Orbitrap Exploris 480 MS for high-throughput analysis of human proteomes and spatial-proteomics revealing phospho-signaling dynamics at subcellular resolution.

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