OpenMS: A Comprehensive Toolbox for Mass Spectrometry Data Analysis

OpenMS is a powerful framework that provides an open-source software library and python bindings, as well as an infrastructure for rapid development of mass spectrometry-related software. The toolbox offers a rich set of tools that can be flexibly combined into powerful analysis workflows, supporting several workflow systems including KNIME, Galaxy, and Nextflow.

OpenMS Tools:

• TOPP: The OpenMS Proteomics Pipeline provides a range of tools for protein identification, quantification, and characterization.
• TOPPView: TOPPView enables the visualization of MS data, allowing users to explore and understand their results in an intuitive way.
• MetaProSIP: MetaProSIP is a tool for automated inference of elemental fluxes in microbial communities, enabling researchers to study metaproteomics data.
• DIAMetAlyzer: DIAMetAlyzer generates targeted assays for metabolomics, streamlining the analysis of small molecules.
• DIAproteomics: DIAproteomics is a workflow for Data-Independent Acquisition (DIA) MS and statistical post-analysis, enabling researchers to analyze complex proteomic data sets.
• Nucleic Acid Analysis: NASE is a nucleic acid search engine that supports RNA and DNA mass spectrometry analysis.
• Protein-Protein Interactions: OpenPepXL enables the study of protein-protein interactions, providing insights into biological processes.

Benefits:

• Flexibility: OpenMS provides a modular framework that allows users to combine tools in various ways to create customized workflows.
• Reproducibility: The toolbox enables reproducible computational analysis, ensuring that results are consistent and reliable.
• Comprehensive Analysis: OpenMS offers a wide range of tools for different types of mass spectrometry data analysis, making it a one-stop solution for researchers.

FLASH Suite for Top Down Proteomics:

• Top-Down MS Data Analysis: FLASHDeconv, FLASHIda, and FLASHQuant provide tools for top-down MS data deconvolution, intelligent data acquisition, and quantification. See details here.

Selected Workflows:

• HLA Ligand Atlas: A comprehensive collection of tissue and HLA allele-specific HLA ligands that are naturally presented.
• MHCquant: A workflow for identification and quantification of HLA ligands.
• quantMS: A workflow for quantitative mass spectrometry analysis.

By using OpenMS, researchers can streamline their mass spectrometry data analysis, gain deeper insights into biological processes, and accelerate discovery in various fields.

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Development and maintenance partially funded by de.NBI.