Fabia Simona from our Product Support team shows you how to set up a DIA analysis in Spectronaut and gives valuable tips on setting up the software for optimal performance on you computer.

SILAC experiments as well as the use of isotopically labeled reference peptides require specific changes to your experiment setup in Spectronaut. Tejas Gandhi from our R&D team walks you through the relevant search and library settings so that you can take advantage of labeled experiments.

One of the most popular features of Spectronaut is directDIA, allowing you to run DIA analysis without additional files for library generation. In this video tutorial, Fabia Simona from our Product Support team demonstrates how to run directDIA in two steps, first generating a library from DIA data, and then using that library for DIA analysis.

Spectronaut offers powerful features to handle large datasets. Maximilian Helf from our R&D department shows you how to queue up analysis jobs in pipeline mode and introduces SNE Combine, a functionality that allows merging results from multiple Spectronaut analysis runs.

Spectronaut command line enables you to run analyses without manual interaction, for instance from scripts. Maximilian Helf from our R&D team shows you how to use Spectronaut command line mode for different workflows, including directDIA and library generation.

Spectronaut uses the HTRMS file format for high performance data analysis. Oliver Bernhard from our R&D team shows you how to save up to 60% analysis time by converting your files into HTRMS format

Getting detailed information on peptide-spectrum matches (PSMs) is important to verify identifications and access to PSM information is required for data submission to many journals and data repositories. Lynn Verbeke from our R&D team shows you how to inspect peptide-spectrum matches in both Spectronaut and SpectroMine.

Spectronaut features extensive support for PTM studies including site-based PTM localization probabilities, quantification, regulation analysis and reporting. Monika Puchalska from our Product Support team shows you how to set up PTM analysis in Spectronaut using phosphorylation as an example.

This seminar at ASMS 2020 Reboot, had two exceptional speaker: Prof. Jesper Olsen and Prof. Florian Meier. First, Prof. Olsen shows, among other great results, how the combination of FAIMS with single CVs, data independent acquisition (DIA) and the new directDIA 2.0 in Spectronaut 14 provides, without any library, results that are comparable to the ones obtained using comprehensive project-specific libraries in older versions of Spectronaut. Then, Prof. Meier elaborates on the benefits of recently developed acquisition methods in DIA mode, supported in Spectronaut 14, such as BoxCar DIA and dia-PASEF. These are specifically thought for optimizing ion acquisition to help overcome traditional limitations such as high dynamic range and scarce samples.

This seminar at ASMS 2020 Reboot had the participation of two outstanding Spectronaut advocates: Prof. Birgit Schilling and Prof. Yansheng Liu. First, Prof. Schilling shows how she uses Spectronaut and directDIA 2.0 to get the best library strategy for her challenging plasma exosomes samples. Later, Prof. Liu presents several different projects where he uses Spectronaut and directDIA, Spectronaut’s dedicated pSILAC workflow, as well as Spectronaut’s recent PTM localization algorithm with very successful results for his challenging samples.

Various studies in the last years have shown that using SRM/MRM has the potential to identify hundreds of biomarker candidates in one study (Mermelekas, 2015). However, panel development remains asignificant bottleneck in the adoption of targeted proteomics.

Presenter: Tejas Gandhi

Date: Wednesday, Sep 20, 2023, 11:45 AM – 1:00 PM
Session: PP05

New: Spectronaut^® 19

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New: Spectronaut^® 19

Unlock Your Data's True Story

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