NucleoSpec Nucleic Acid-Silver Complex & Cluster Analyzer

What is NucleoSpec?

NucleoSpec is a web-based tool for assigning compositions to negative-mode ESI mass spectra of nucleic acid–metal complexes.

Given a spectrum and a nucleic acid sequence (or formula), NucleoSpec will:

• Auto-detect charge states from isotope spacing
• Search for matching compositions (strand count, metal count, N₀, Q_cl)
• Generate theoretical isotope patterns for visual overlay comparison
• Handle adducts (Na⁺, NH₄⁺, Cl⁻, custom) automatically

Supports DNA-Ag_N, complex DNA/XNA, and custom XNA (TNA, PNA, LNA, etc.) modes.

Upload Data

• This tool is designed for negative mode ESI-MS data
• Supported formats: .txt or .csv
• Two columns: m/z (mass-to-charge) and intensity
• Tab or space separated
• Example:

  500.123    1000
  500.624    850
  501.125    600

• Drag & drop file or click "Select File"
• Resolution is auto-detected from your spectrum

Choose Analysis Mode

Three modes available:

Analyze Peaks

• Click any peak in the spectrum to analyze it
• Charge state (z) is auto-detected based on isotope spacing
• Color-coded markers indicate charge state (see legend on spectrum)
• Small peaks (< 1% intensity) may not show markers but can still be clicked
• Zoom in to double-check the charge state assignment
• If the Gaussian fit looks poor, use manual fitting to adjust
• Composition matches appear in the "Composition Analysis" section below

Understanding Results

Each composition result shows these key parameters:

Overlay & Compare

• Check the box next to any composition to overlay its theoretical isotope pattern
• The overlay appears in the zoom plot on a secondary y-axis
• A good match: theoretical peaks align with experimental peaks in m/z position
• A poor match: peaks are shifted or the envelope shape doesn't match
• Multiple overlays can be shown at once to compare candidates
• If the best fit overlay looks offset, try the neighboring N₀ values

Advanced Features

Tips & Troubleshooting

• No peaks detected? Check file format – ensure two columns (m/z, intensity)
• Poor matches? Try manual Gaussian fitting or custom composition search
• Wrong charge state? Zoom in to verify isotope spacing, then re-analyze with correct z
• Overlay looks offset? The neighboring N₀ value may be a better match – check by overlaying it
• Odd N₀ warning? Stable DNA-Ag_N clusters typically have even N₀; odd values may indicate a calibration issue
• Start fresh? Click "Reset Analysis" to clear all data
• Data privacy: Uploaded spectra are processed on the server but are not stored – all data is discarded after analysis