Join our Spectronaut User Meeting in Boston for a full day of expert talks, Spectronaut workshop, and interactive discussions at the Broad Institute.
Connect with fellow researchers and the Biognosys team to explore best practices, advanced workflows, and the latest innovations in proteomics data analysis. Our team will also lead a 90-minute Spectronaut workshop with live Q&A, offering practical guidance and the opportunity to address your specific questions.
Gain practical insights, share experiences, and deepen your expertise in a collaborative setting. We look forward to seeing you there!
Wednesday, April 8, 2026
9:00 AM – 6:00 PM
The Broad Institute
300 Binney Street (Room 2110 – Charles)
Cambridge, MA 02142
USA
9.00 – 9.45 AM Welcome & Coffee
9.45 – 10.15 AM ”Spectronaut: Developments and Directions” by Tejas Gandhi, PhD (Biognosys)
10.15 – 10.45 AM ”Parallelizing Spectronaut directDIA” by Cameron Lian and Natalie Clark, PhD (The Broad Institute)
10.45 – 11.15 AM Coffee Break
11.15 – 11.45 AM ”Spectronaut in Industry: Empowering High-Throughput Proteomics and Cross-Functional Collaborations” by Jan Schejbal, PhD (AbbVie)
11.45 – 12.15 PM ”Enabling large-scale proteomic analysis of biofluids for the identification of biomarkers for amyloid conversion and early cognitive decline in matched plasma and CSF samples” by Jan Muntel, PhD (Biognosys)
12.15 – 13.30 PM Lunch (provided)
13.30 – 14.00 PM ”Quantifying and Understanding Phosphoproteome Turnover: From In Vitro to In Vivo” by Yansheng Liu, PhD (Yale)
14.00 – 14.30 PM ”Deciphering Protein Corona Assembly and Non-Canonical Translation of mRNA-LNPs Through Advanced Mass Spectrometry” by Joseph McLaughlin and Zon Weng Lai, PhD (Sanofi)
14.30 – 15.00 PM ”From Discovery to Clinical Translation: High-Precision Protein Quantification with SISCAPA Immuno-MS” by Morty Razavi, PhD (SISCAPA)
15.00 – 15.15 PM Coffee Break
15.15 – 16.45 PM Spectronaut Workshop
16.45 – 18.00 PM Networking
Yansheng Liu, PhD, Associate Professor, Department of Pharmacology and Biomedical Informatics & Data Science (BIDS), Yale University School of Medicine
”Quantifying and Understanding Phosphoproteome Turnover: From In Vitro to In Vivo”
Proteins are not only regulated by how much they are made, but also by how long they last. Our work reveals that dynamic phosphorylation not only marks signaling events but also may modulate protein lifespans. Starting from our early DeltaSILAC studies in cells and extending to recent in vivo turnover atlases, I will illustrate how phosphoproteome dynamics shape tissue-specific proteostasis beyond steady-state abundance. I will also highlight how multiplexed DIA-MS, together with a dedicated bioinformatic pipeline, enables turnover-resolved views of protein and phosphorylation dynamics.
Jan Schejbal, PhD, Senior Scientist I, QTAS MS Proteomics, AbbVie
”Spectronaut in Industry: Empowering High-Throughput Proteomics and Cross-Functional Collaborations”
This presentation will highlight the central role of Spectronaut and SpectroMine in modern proteomics data analysis and reporting workflows. Through selected case studies, the first part of the talk will demonstrate how Spectronaut’s advanced analysis and visualization capabilities support the management of large-scale studies, enable cross-functional collaboration, and facilitate access to insights generated from proteomics experiments.
In the second part, the presentation will explore how SpectroMine and Spectronaut are supporting the implementation and onboarding of MHC-associated peptide proteomics (MAPPs) workflows, helping to streamline analysis and accelerate adoption in complex research settings.
Cameron Lian, Research Associate I, Proteomics Platform, the Broad Institute
Natalie Clark, PhD, Senior Computational Scientist, Proteomics Platform, the Broad Institute
”Parallelizing Spectronaut directDIA”
Library-free data-independent acquisition (DIA) proteomics analysis is computationally expensive at large scale, creating a critical bottleneck in translating mass spectrometry data into biological insights. To address this challenge, we developed an out-of-the-box, cloud-native workflow that parallelizes Spectronaut directDIA analysis on Google Cloud Platform via Terra, achieving more than a 20-fold runtime improvement at lower cost compared to conventional single-node workflows. Beyond parallelization, this workflow offers extensive flexibility for users to set up analyses per their experimental needs. Our rigorous benchmarking on data acquired from both Thermo Fisher Orbitrap and Bruker timsTOF platforms confirmed remarkable consistency with conventional workflows in both identification and quantification performance.
Joseph McLaughlin, Research Associate – Bioanalytics & DMPK, Research & Biomarkers, Yoh Assigned at Sanofi
Zon Weng Lai, PhD, Associate Director – Bioanalytics & DMPK, Research & Biomarkers, Sanofi
”Deciphering Protein Corona Assembly and Non-Canonical Translation of mRNA-LNPs Through Advanced Mass Spectrometry”
mRNA-LNP technology represents one of the most significant breakthroughs in modern medicine, transforming how we approach vaccines and therapeutics. However, challenges in LNP thermostability, tolerability, and how to best deliver mRNA payload make up some of the most pressing problems across the industry. Utilizing advanced mass spectrometry, we help to unravel the mechanisms behind our mRNA-LNPs performance to effectively address these challenges.
Jan Muntel, PhD, Vice President of Scientific Operations, North America, Biognosys
”Enabling large-scale proteomic analysis of biofluids for the identification of biomarkers for amyloid conversion and early cognitive decline in matched plasma and CSF samples”
Reliable biomarkers for Alzheimer’s disease (AD) are urgently needed to identify individuals at the very earliest stages of disease. Previous efforts have often lacked the analytical depth to discover robust biomarkers and data analysis capabilities to analyze 100s to 1’000s of files. By the application of P2 and P1 enrichment techniques, we quantified more than 6’500 proteins in plasma and more than 3’500 proteins in CSF in 600 matched patient samples. With OmicsFlow these data were analyzed in a few days and the proteomic profiles revealed molecular alterations in both plasma and CSF that preceded amyloid conversion and cognitive decline.
Morty Razavi, PhD, COO, SISCAPA
”From Discovery to Clinical Translation: High-Precision Protein Quantification with SISCAPA Immuno-MS”
Bridging discovery proteomics and regulated bioanalysis remains a critical bottleneck in drug development. This presentation highlights how SISCAPA technology enables robust, automation-ready, multiplexed protein quantification with absolute accuracy—supporting biomarker validation, target engagement studies, and clinical decision-making.
Tejas Gandhi, PhD, Vice President Bioinformatics, Biognosys
”Spectronaut: Developments and Directions”
Biognosys AG
Wagistrasse 21
8952 Schlieren
Switzerland
Phone: +41 44 244 50 00
US Offices
Biognosys Inc
70 Bridge St, Suite 104
Newton, MA 02458
United States
