Spectronaut 19

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Spectronaut 19 The gold standard for DIA proteomics analysis

Thanks to deep-learning augmented peptide identification, you can now find more precursors and proteins in your samples than ever before. We have further broadened our support for the latest mass spectrometry data acquisition technologies, and provide new ways to quickly and thoroughly analyze data.

SKU: 2408087 Category: Science Research

Description

Spectronaut 19

The gold standard for DIA proteomics analysis

Spectronaut^® is a commercial software package aimed at analyzing data-independent acquisition (DIA) proteomics experiments. Spectronaut^® can quantitatively profile 100s to several 1,000s of proteins in one experiment. Large experiments with several conditions and replicates consisting of up to 10,000s of LC-MS runs can be analyzed.

Features:

Vendor Independent
Usability
Complete Workflow
Performance and Scalability
Versatility and Flexibility

Spectronaut™ has been providing the best solution for data analysis of DIA experiments in recent years. The latest version of Spectronaut seamlessly integrates multiple independent DIA-related analysis processes, which better expands the application field of Spectronaut.

Spectronaut® is a tool designed to analyze independent data acquisition (DIA) proteomics experiments. Spectronaut can analyze hundreds to thousands of proteins. Large experiments with multiple conditions and can analyze replicates consisting of up to tens of thousands of LC-MS runs.

Spectronaut can analyze DIA data without using a retention time calibration kit. However, it is strongly recommended to add an iRT kit because it ensures calibration on difficult matrices and allows detailed quality control readings.

1. Building a mixed library

By combining large-scale spectral libraries from other sources (project or resource libraries) and the DIA detection data of the sample itself (directDIA), a large number of quantitative proteins can be obtained without building a library yourself.

2. Adding labeling workflow

When mixing Biognosys’ new PQ500 isotope labeled peptide kit, the target protein can be absolutely quantified by non-labeled quantification and can span 5 orders of magnitude.

3. Host cell protein

By correcting for residual proteins, low-abundance host cell proteins can be qualitatively and quantitatively analyzed with high accuracy.

“Spectronaut X can integrate DDA and DIA data during the process of building a mixed library. In our practice, we found that we can get better results and develop new data acquisition strategies.”

Spectronaut®19 main release features

1 Major improvements in directDIA

• Improved scoring: Based on a large and diverse DIA dataset, the average proteome increased by 10% and the precursor increased by 13%

• Improved quantification: Based on a large and diverse controlled quantitative experiment, the number of true candidates increased by 11%.

2 Powered by AI

• Up to 40% improvement in key performance metrics for deep learning models

• Optional use of deepQuant, a deep learning-based interference correction algorithm

• Improved inference for a range of modifications and tags, such as dimethylation, ubiquitination, mTRAQ, and more.

3 Significantly improved computational performance

• directDIA is 40% faster on timsTOF and Astral data compared to Spectronaut 18.0

• Reduced directDIA RAM usage: 90% reduction in memory growth. In theory, 512 GB of RAM can process 10,000 samples using directDIA plus

SNECombine workflows.

• Spectronaut saved experiment (.SNE) file size reduced by up to 80%

• Temporary hard disk requirements reduced by up to 86% (directDIA from HTRMS)

• Temporary hard disk requirements reduced by up to 50% (directDIA from native vendor format)

4 New acquisition method support

• diagonal-PASEF support for directDIA and library-based analysis on Bruker’s timsTOF platform

• New visualization of diagonal-PASEF in the analysis perspective

5 Improved support for tag DIA workflows

• Added support for run-level channel q-values

• Annotation of biological conditions at the channel level

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-Biognosys Confidential 6 New features for analysis of post-translational modifications

• Input normalization by linking enrichment experiments to non-enrichment experiments

• Support for site occupancy calculations

• New visualizations in the analysis and post-analysis perspectives

7 Improved command line interface

• New SNEMerge Options facilitate batch or parallel processing: merge multiple

SNE files into one SNE file

• New option for input normalization

• Immediate exit if command has error

• Use separate command with clear option range for each pipeline

• Enhanced POSIX compatibility

8 new visualizations and reports

• Elution group level  EG.InputNormalizationFactor

• Elution group level  EG.QuantityPerProtein

• PTM site report  PTM.QuantityPerProtein

• PTM site report  PTM.InputNormalizationFactor

• PTM site report  PTM.Stoichiometry

• New R.PTMSites category lists all identified sites for each PTM

• Peptide vs. protein quantity plot

• Post-analysis overview average PTM localizations

• Sample links page in Experimental Settings

9 new and changed analysis settings

• [NEW] DIA Analysis  PTM Workflow  Input Normalization Strategy

• [NEW] DIA Analysis  PTM Workflow  PTM Localization  Chemometrics

Computational Strategies

• [NEW] DIA Analysis  Quantification  DeepQuant Correction [Beta]

• [NEW] DIA Analysis  Workflow  Hybrid (DDA + DIA) Libraries

• [NEW] directDIA  Pulsar Search  Acceleration  diaPASEF Processing  Fast

• [NEW] directDIA  Pulsar Search  Identification  directDIA Workflow  RT

Sampling Reduction

• [CHANGE] Spectronaut 19 uses only MS2 quantification for differential abundance analysis.

Previously, the default was to use both MS1 and MS2

Spectronaut 19

Spectronaut 19 The gold standard for DIA proteomics analysis

Spectronaut 19

The gold standard for DIA proteomics analysis

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