fancyMS2viewer

A fast, publication-friendly desktop viewer for MS/MS (MS2) spectral libraries — browse, search, filter, richly style, and export tandem mass spectra.

Reads .msp, .mgf, .mzML · handles multi-GB files · vector PDF export · zero install on Windows

⚠️ Built entirely by AI. All of the code, the icon, and this README were written by Anthropic's Claude (via Claude Code) through an iterative conversation, as a demonstration of AI-assisted software development. Please review before relying on it for critical work.

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Screenshot

The main window on a 2.98 GB Bruker timsTOF .mzML (165,768 scans → 155,568 MS2 kept, MS1 skipped) — it streams in about 18 s and stays interactive. Here the m/z filter narrows it to the 29 precursors matching 653.681 ± 10 ppm:

Everything on the plot is styleable, on screen and in exports — background theme, peak colours, draggable metadata labels, per-element fonts & colours:

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Features

Formats & performance

• Reads .msp (NIST), .mgf (Mascot Generic Format) and .mzML (incl. .gz); format auto-detected.
• Streaming background load — spectra appear as they parse (progress in the status bar); the UI never freezes.
• Built for very large mzML (multi-GB timsTOF / Orbitrap): MS1 scans are skipped, peaks stored in compact arrays, strings interned.
• Open several files at once, or drag-and-drop onto the window.

Browse, search & filter

• Spectrum list with a configurable label field and numeric-aware sort.
• Multiple search boxes combined with All (AND) / Any (OR); each box matches a field by contains (text), range, or value ± tolerance.
• m/z filter on the precursor or any fragment peak, tolerance in ppm or Da. Type an m/z, or compute it from a chemical formula + adduct (monoisotopic mass) plus an optional extra Δmass.
• Default view limited to precursor + 5 m/z (toggleable).
• Metadata panel with a show/hide field chooser.

Interactive plot

• Zoom X and Y — drag a box, or scroll the wheel (over an axis end it pins that end); pan by dragging the axes; double-click to reset one axis or all.
• Hover for exact m/z / intensity; the Y axis does not rescale when you zoom X.

Styling — applied on screen and in every export

• Peak colours: preset schemes (Ocean, Viridis, Magma, Sunset, …) or a fully custom single colour / multi-stop gradient with a colour palette and draggable stop positions.
• Adjustable bar thickness and transparency.
• Plot background themes: White, Light grey, Sepia, Dark, Black.
• Metadata labels on the plot — add any field as value only or Field: value; drag to move, wheel to resize, right-click / double-click to edit; per-label font size, bold, italic, colour. They stay put across spectra and just update their values.
• Axes & labels — show/hide ticks, titles and peak labels; editable X/Y titles; independent per-axis title font size / bold / italic / colour; tick and peak-label font / bold / italic / colour; peak-label count auto (by spacing) or fixed.
• Toggle relative (%) vs absolute intensity.
• Text renders in Arial (Latin) and Microsoft YaHei (Chinese), with bold/italic, embedded as subsets in exported PDFs.

Export

• Copy peaks to clipboard as two columns (m/z + intensity) — paste into Excel.
• Save spectra to .msp / .mgf (a multi-selection goes into one file).
• Save the plot as PNG (raster) or vector PDF (one page per spectrum), at the current preview size or a custom size — with a live preview:

• Right-click a spectrum (list) or the plot to export directly.

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Getting started

Windows (no install)

Download fancyMS2viewer.exe (see the dist/ folder or the Releases page) and double-click it — everything is bundled, no Python needed. You can also drag .msp / .mgf / .mzML files onto the window or the .exe icon.

Run from source

python fancyMS2viewer.py            # then File → Open…
python fancyMS2viewer.py file.mzML  # open a file directly

Requirements (Python 3.9+): tkinter (stdlib) · Pillow (PNG) · reportlab (vector PDF) · tkinterdnd2 (optional, drag-and-drop).

pip install pillow reportlab tkinterdnd2

Missing optional packages degrade gracefully.

Build the executable

pip install pyinstaller
pyinstaller --noconfirm --onefile --windowed \
  --icon icon.ico --add-data "icon.png;." \
  --name fancyMS2viewer fancyMS2viewer.py

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Notes

• The mzML reader keeps only MS2 (and higher) spectra; MS1 survey scans are skipped by design.
• Tested on Windows; the source is cross-platform, but the packaged .exe and the bundled fonts (Arial / Microsoft YaHei) are Windows-oriented.

License

Released under the GNU General Public License v3.0 — see LICENSE.

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_{Made with 🤖 by Claude (Anthropic) via Claude Code.}