FragPipe

FragPipe analyzes mass spectrometry-based proteomics data and integrates TMT-Integrator for processing isobaric quantitative proteomic data from TMT and iTRAQ experiments.

Key Features:

• Multiplex Quantitative Proteomics Support: Processes quantitation results from TMT and iTRAQ experiments, including TMT 35-plex reagents.
• Integrative Reporting: Generates reports at gene, protein, peptide, and post-translational modification site levels.
• MSFragger Integration: Leverages MSFragger as the core search engine for proteomics data analysis.
• Phosphoproteome Analysis: Identifies phosphorylated sites in phosphopeptide-enriched datasets.
• Performance Benchmarking: Quantifies more proteins and delivers more robust quantification performance compared to MaxQuant and Proteome Discoverer.

Scientific Applications:

• Spike-in Protein Quantification: Analyzes datasets with controlled protein spike-ins, such as E. coli with 13 spike-in proteins.
• Cancer Proteomics: Analyzes clinical proteomic tumor datasets, including clear cell renal cell carcinoma whole proteome and phosphoproteome data.
• Advanced Instrument Analysis: Processes data from latest mass spectrometry advances, including the Astral instrument.
• Comparative Performance Evaluation: Benchmarked against other tools using OmicsEV for validation of quantification accuracy and robustness.

Methodology:

TMT-Integrator processes quantitation results from TMT and iTRAQ experiments as a core component integrated into the FragPipe computational platform.