README.md

metadata

title: NucleoSpec
emoji: 🔬
colorFrom: blue
colorTo: purple
sdk: docker
app_port: 7860
pinned: false
license: cc-by-nc-4.0
short_description: ESI-MS analysis of nucleic acid-silver complexes

NucleoSpec

Nucleic Acid-Silver Complex & Cluster Analyzer

A web-based application for analyzing nucleic acid (DNA/XNA)-silver complexes and nanoclusters from mass spectrometry data.

Project Structure

NucleoSpec/
├── dna_silver_webapp.py       # Main Flask application
├── core/
│   ├── analyzer.py            # DNASilverAnalyzer class (composition search)
│   ├── spectrum.py            # SpectrumMixin: parsing, peak detection
│   ├── envelope.py            # EnvelopeMixin: Gaussian fitting, symmetry
│   ├── scoring.py             # ScoringMixin: pattern similarity, scoring
│   ├── isotope.py             # IsotopeMixin: isotope pattern generation
│   ├── charge.py              # ChargeMixin: charge state detection
│   ├── adducts.py             # AdductMixin: custom adduct CRUD
│   └── dna.py                 # DNAMixin: DNA/XNA composition helpers
├── lib/
│   └── pythoms/               # PythoMS library (isotope calculations)
├── templates/
│   └── index.html             # Single-page frontend (Plotly.js, JSME)
├── sample_data/               # Example spectrum files
└── environment_hf.yml         # HuggingFace deployment environment

Installation

conda env create -f environment.yml
conda activate dna_mass_spec
python dna_silver_webapp.py

Open http://localhost:8080 in browser.

Analysis Modes

DNA-Ag_N Mode

For single-stranded DNA-silver nanoclusters.

• Enter DNA sequence using A, T, G, C bases
• Automatically calculates molecular composition
• Uses N₀/Qcl framework for cluster characterization

Ag(I)-DNA/XNA Complex Mode

For double-stranded DNA or DNA/XNA hybrids.

• DNA Complex: Enter two DNA sequences (Strand 1 and Strand 2)
• XNA Complex: Check "Use XNA" and enter two molecular formulas
  • Formulas are automatically combined by adding atoms

XNA-Ag_N Mode

For custom xeno nucleic acids (TNA, PNA, LNA, etc.).

• Enter XNA name for identification
• Enter complete molecular formula (e.g., C₁₀₀H₁₂₀N₄₀O₆₀P₁₀)
• Optionally use JSME structure drawer to get formula

Workflow

1. Select Mode - Choose DNA-Ag_N, Ag(I)-DNA/XNA Complex, or XNA-Ag_N from the mode selector
2. Upload Spectrum - Click "Choose File" and select your mass spectrum file
3. Enter Information - Provide DNA sequence or XNA formula based on selected mode
4. Apply Settings - Click the "Apply" button to confirm your settings
5. Analyze Peaks - Click any peak in the spectrum to find matching compositions
6. Compare Results - Toggle checkboxes to overlay theoretical isotope patterns on the experimental data

File Format

Spectrum files should be two-column format (tab or comma separated):

m/z         intensity
1000.123    45678.9
1000.456    56789.0
1001.234    67890.1

Supported formats: .txt, .csv

Output Fields

Field	Description
Formula	Neutral molecular formula of the cluster
Ion Formula	Charged species formula (can be copied)
nAg	Number of silver atoms in the cluster
N₀	Number of effective valence electrons
Qcl	Charge of inorganic core
z	Charge state of the detected ion
ΔX₀	Difference between experimental and theoretical centroid (lower = better match). Primary criterion for Best Fit selection.
Pattern similarity	Mean of cosine similarity and Pearson correlation between experimental and theoretical isotope envelopes (0–1). Confidence indicator: ▲ > 0.8 high, ○ 0.5–0.8 moderate, ▽ < 0.5 low

Features

• Charge Detection - Automatic charge state determination from isotope spacing
• Isotope Pattern Matching - Compare experimental peaks with theoretical patterns
• Adduct Support - Account for common adducts (NH₄⁺, Na⁺, Cl⁻) plus user-defined custom adducts
• Structure Drawing - JSME molecule editor for drawing bioconjugate structures
• Data Export - Download theoretical spectra as CSV files

Technical Details

• Backend: Python 3.12, Flask, NumPy, SciPy
• Frontend: HTML5, JavaScript, Plotly.js, JSME
• Libraries: PythoMS, IsoSpecPy

Citation

If you use NucleoSpec in a publication, please cite:

Lin, I.-H.; Copp, S. M. A Tutorial on Automated Mass Spectral Analysis using NucleoSpec for Compositional Assignment of Nucleic Acid–Silver Complexes and Nanoclusters. ChemRxiv 2026. DOI: 10.26434/chemrxiv.15004738/v1

Support

• Developer: I-Hsin (Vivian) Lin
• Email: ihl1@uci.edu
• Lab: Copp Lab, University of California, Irvine