Aerith

Aerith visualizes and annotates isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics mass spectrometry data.

Key Features:

• Isotopic Envelope Visualization: Visualizes simulated and observed isotopic envelopes of peptides and metabolites with user-defined formula and atom % enrichment levels.
• Peptide Isotopic Peak Visualization: Visualizes peptide isotopic peaks from mass spectrometry data.
• SIP Peptide-Spectrum Match Visualization: Visualizes stable isotope probing peptide spectra match (PSM) results.
• PSM Quality Filtration: Filters high quality peptide-spectrum matches for confident identification.
• Accurate Isotopic Abundance Calculation: Calculates accurate isotopic abundance of peptides and metabolites using FFT-based and Monte Carlo algorithms.
• Peptide-Spectrum Match Evaluation: Evaluates PSMs through multiple robust and commonly used scoring functions to compare experimental and theoretical spectra.
• Isotopic Fine Structure Simulation: Simulates fine isotopic structures of compounds using Monte Carlo simulation via the multinomial distribution.
• Metabolite Isotopic Envelope Calculation: Calculates isotopic envelopes of metabolites with known chemical formulas using an FFT-based algorithm.
• Fragment Ion Series Modeling: Models isotopic distributions of fragment ion series of peptides by sequentially convoluting isotopic envelopes of monomeric units using a convolution algorithm.
• SIP Proteomics Results Visualization: Visualizes stable isotope probing proteomics results for data interpretation.

Scientific Applications:

• Stable Isotope Probing Proteomics: Enables precise annotation of mass spectra and manual validation of peptide identifications in proteomic SIP studies using 13C, 15N, or 2H labeled substrates.
• Stable Isotope Probing Metabolomics: Supports accurate simulation and visualization of isotopic envelopes for metabolite identification in metabolomic SIP studies.
• Isotopic Fine Structure Resolution: Resolves isotopic fine structures and envelopes for compounds such as glucose, penicillin, and microbial peptides containing natural and enriched isotopes.
• Metabolic Tracing: Traces metabolism of biological cells using isotopically heavy substrates through visualization of partially labeled peptides and metabolites.

Methodology:

Aerith models isotopic distributions of peptide fragment ion series by sequentially convoluting isotopic envelopes of monomeric units using a convolution algorithm. It simulates fine isotopic structures via Monte Carlo simulation through the multinomial distribution, and calculates metabolite isotopic envelopes using an FFT-based algorithm. Peptide-spectrum matches are evaluated through multiple robust scoring functions comparing experimental and theoretical spectra. Algorithms were implemented in C++ and accessed in R via Rcpp.