dasmixer 0.3.0

No project description provided

DASMixer

DASMixer is a cross-platform desktop application for integrating and comparing peptide identification data from mass spectrometry experiments. It is designed to merge de novo sequencing results with library search identifications, perform full comparative proteomics workflows, and produce publication-ready reports.

Developed at the Laboratory of Structural Proteomics, IBMC, Moscow.

---

Key Features

Data Loading

• Import spectra files in MGF format (MZML support planned)
• Import peptide identification results from:
  • PowerNovo 2 (de novo sequencing)
  • MaxQuant (Evidence files)
  • PLGS (Waters library search)
• Manage multiple spectra files and identification files per project
• Assign samples to comparison groups (subsets) for differential analysis
• Multi-file batch import via file-pattern matching (CLI & GUI)

Peptide-Level Processing

• Merge and evaluate identifications across tools
• Set thresholds: PPM error, score, intensity coverage, sequence length, peak counts
• Calculate ion coverage (a, b, c, x, y, z ion types) with configurable parameters:
  • Water/ammonia loss ions
  • PPM-based matching tolerance
• Automatic best-charge and isotope-offset correction for de novo sequences
• Select preferred identification per spectrum (by PPM or intensity coverage)
• Interactive ion annotation plots via Plotly + PyWebView

Protein-Level Processing

• Map peptides to protein sequences using FASTA files (via npysearch BLAST-like search)
• Support for partial sequence matches (for de novo identifications)
• Filter protein identifications by peptide count, unique evidence count
• Compute sequence coverage per protein per sample
• LFQ quantification: emPAI, iBAQ, NSAF, Top3 (via semPAI library)
• UniProt data enrichment (via uniprot-meta-tool)

Reports and Export

• Built-in reports: PCA, Volcano plot, UpSet plot, Coverage report, Tool comparison, Sample summary
• Interactive preview in PyWebView
• Export to HTML, XLSX, DOCX formats
• Saved plots with configurable dimensions and font sizes
• Report history stored in project file

Plugin System

• Install custom identification parsers (.py or .zip packages)
• Install custom report modules
• Manage plugins via GUI Plugins panel.

---

Installation

From PyPI

pip install dasmixer

Development setup (Poetry)

git clone [e-mail]:protdb/dasmixer.git
cd dasmixer
poetry install
poetry run dasmixer

Standalone windows executable:

Download latest version

Then you should unpack the archive and run dasmixer.exe from unpacking folder

Requirements: Python ≥ 3.11

---

Usage

Read the instruction

Also check out the guide for the process here

Launch GUI

dasmixer                          # Start with empty screen
dasmixer project.dasmix           # Open existing project in GUI

Architecture

Layer	Technology
GUI	Flet 0.80.5
CLI	Typer
Interactive plots	Plotly + PyWebView
Data processing	Pandas, NumPy
Proteomics	Pyteomics, Peptacular, Npysearch
Project storage	SQLite (aiosqlite, async)
Configuration	Pydantic-settings
Export	openpyxl, html-for-docx, Kaleido

The application exposes three parallel interfaces:

• GUI — desktop application window
• CLI — command-line tool (dasmixer)
• Python API — importable package for scripting

---

---

Project File Format

Projects are stored as single SQLite files with the .dasmix extension. The database contains:

• Project metadata and settings
• Spectra (MGF data as compressed NumPy arrays)
• All identification data
• Protein sequences and identification results
• LFQ quantification results
• Generated reports and saved plots

---

Documentation

Document	Description
docs/project/MASTER_SPEC_NEW.md	Full project specification and architecture overview
docs/api/	API reference for the Python package
docs/gui/	GUI architecture and components
docs/user/	User guides (workflow, identification, proteins, reports)
AGENTS.md	AI agent development guide

---

License

Copyright © Laboratory of Structural Proteomics, IBMC, Moscow. All rights reserved.