GeenaR

GeenaR analyzes Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectra to preprocess, compare, visualize, and extract proteomic features for biomarker identification and related analytical applications.

Key Features:

• Complete workflow: Integrated workflow encompassing pre-processing, analysis, visualization, and comparison of MALDI-TOF mass spectra.
• Advanced spectral processing: Functions for extracting relevant spectral characteristics from noisy datasets and addressing common mass-spectrometry noise interferences.
• Reproducible research support: Generation of human-readable reports that document function parameters, results, and the code used during processing.
• Case study demonstrations: Applied analyses exemplified on oncological datasets, specifically ovarian cancer and colorectal cancer.

Scientific Applications:

• Proteomics sample characterization: Characterization and identification of biological samples using MALDI-TOF spectra.
• Cancer biomarker identification: Discovery and comparison of spectral features associated with cancers such as ovarian and colorectal cancer.
• Food fraud detection: Detection of adulterants and verification of food product authenticity via mass spectral analysis.
• Doping substance detection: Identification of banned substances in biological fluids using MALDI-TOF spectra.

Methodology:

Computational steps explicitly include pre-processing, noise and bias handling, spectral analysis, visualization, comparison of spectra, and generation of reports documenting parameters, results, and code.