E-Poster 1374/5 presented at AACR 2022

Presenter: Marco Tognetti
Session: PO.IM01.05 – Tumor Antigens, Antigen Presentation, and Tumor Immunity
Date: April 11

In this webinar, Andreas-David Brunner presents a robust and scalable single-cell DIA proteomics workflow using ion mobility technology (dia-PASEF), developed at the Max Planck Institute of Biochemistry (Matthias Mann Lab). The team quantified up to 1,500 proteins in a drug perturbation experiment using Spectronaut – the gold standard software for DIA proteomics. In a second step, they compared single-cell proteomics data to publicly available single-cell RNA-sequencing data, revealing fundamental differences in regulation between the two modalities.

At this event, Biognosys launches the much-awaited Spectronaut 15. The latest version of the software comes with many novel and improved applications. Oliver M. Bernhardt, the lead developer of Spectronaut, shows you how to take advantage of some exciting new features.

Bruderer R, Bernhardt OM, Gandhi T, Miladinović SM, Cheng L, Messner S, Ehrenberger T, Zanotelli V, Butscheid Y, Escher C, Vitek O, Rinner O, Reiter L. MCP.

In this work, Biognosys and collaborators compared proteome coverage and quantification performance of the emerging DIA/SWATH method against the long-established shotgun DDA. The hyper reaction monitoring (HRM) workflow presented in this work combined DIA acquisition and retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. HRM showed higher precision, accuracy and less missing values compared to DDA and was proposed for large-scale quantitative proteome profiling.

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Mass spectrometry (MS)-based proteomics allows the comprehensive identification and quantification of proteins in various biological specimen such as cell lines, body fluids or tissues. The study of these complex samples for applications like biomarker discovery requires large sample cohorts with low technical variability to overcome inter-individual differences and achieve sufficient statistical power.

Rapid developments in the field of proteomics within recent years have enabled the reproducible and reliable quantification of large sample cohorts. Large scale studies comprising hundreds of samples are primarily processed and analyzed in one centralized facility.

Identifying changes in protein levels against a vast dynamic background of proteins has been an ongoing challenge in proteomics. This technical note demonstrates Spectronaut’s ability to accurately identify biomarkers. Here we use control quantitate experiments (CQE) to benchmark the ability to differentiate true candidate biomarkers using Spectronaut and other leading DIA analysis applications.

Poster MP 074 presented at ASMS 2022

Presenter: Tejas Gandhi
Session: Data-Independent Acquisition
Date: Monday, June 6

Presenter: Tejas Gandhi

Date: Thursday, June 8
Topic area: Data-Independent Acquisition II

New: Spectronaut^® 19

Unlock Your Data's True Story

New: Spectronaut^® 19

Unlock Your Data's True Story

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