MASSyPup

MASSyPup provides an integrated computational environment for processing and analyzing mass spectrometry (MS and MS/MS) data to support protein and metabolite identification, statistical validation, and data mining.

Key Features:

• Integrated Toolset: Includes OpenMS/TOPPAS, Trans-Proteomic-Pipeline programs, ProteoWizard tools, X!Tandem, Comet, and SpiderMass for peak picking and identification of proteins and metabolites.
• Statistical Validation and Metabolomics Processing: Uses the R programming language with packages such as XCMS/metaXCMS and MetabR for MS and metabolomics data processing and validation.
• Data Mining Tools: Provides Rattle and Random Forest implementations for predictive modeling and assessment of variable importance in MS datasets.
• Advanced Data Handling: Provides teapot for editing large datasets and command-line tools for transposing extensive matrices to manage voluminous MS data.
• Workflow Management: Integrates programs and modules using the Taverna Workflow Management System to create and execute reproducible analysis workflows for tasks such as protein identification/validation, peptide association analysis, cluster analysis in targeted metabolomics, and raw data processing for untargeted metabolomics.

Scientific Applications:

• Protein Identification and Validation: Supports workflows that perform peptide association analysis and protein identification for target proteomics and biomarker discovery.
• Metabolomics Analysis: Supports targeted and untargeted metabolomics, including cluster analysis, classification of sample groups, and identification of relevant biological features and pathways.

Methodology:

Computational methods explicitly include peak picking and identification via OpenMS/TOPPAS, ProteoWizard, X!Tandem, Comet and SpiderMass; metabolomics processing and statistical validation with R packages XCMS/metaXCMS and MetabR; data mining with Rattle and Random Forests for variable importance; workflow orchestration with Taverna; and large-matrix editing with teapot and command-line transposition.