Welcome to SynapSpec
SynapSpec is a comprehensive mass spectrum analysis tool designed for both beginners and advanced users. With intuitive GUI and powerful CLI interfaces, it provides everything you need for accurate spectrum processing and compound identification.
🚀 Quick Start
🖥️ GUI Interface
Launch the graphical interface for interactive analysis
Double-click the SynapSpec application icon
GUI Tutorial →💻 CLI Interface
Run analysis with command-line for batch processing
synapspec run config.yaml🔬 Core Features
Peptide Identification & Quantification
Advanced algorithms for accurate peptide identification with robust false discovery rate control and precise quantification across samples.
Deep Learning-based Spectral Library Generation
Advanced deep learning models for accurate spectral library prediction and generation, enabling enhanced peptide identification and DIA analysis.
Label-free Quantification
Support for both label-free and isobaric labeling method for multiplexed quantitative proteomics experiments.
DIA Analysis
Optimized workflows for data-independent acquisition and SWATH-MS analysis with spectral library generation and matching.
Statistical Analysis & Differential Expression
Integrated statistical tools for differential expression analysis and multiple testing correction.
📊 Supported Formats
Input Formats:
- .raw
- .d
- .mzML
Library Formats:
- .txt (MaxQuant format)
- .tsv (MaxQuant format)
Output Formats:
- .csv
- .tsv
- .parquet
🛠️ Installation
Get started with SynapSpec in minutes. Choose your platform: View detailed installation guide →
📖 Popular Documentation
Quick Start Guide
Get up and running in 5 minutes
GUI Tutorial
Interactive analysis with graphical interface
CLI Tutorial
Command-line tools for batch processing
Community Support
Get help and connect with other users
🌟 Need Help?
- 📚 Documentation: Browse our comprehensive guides
- 🐛 Bug Reports: GitHub Issues
- 💬 Discussions: Community Forum
- 📧 Support: contact@bionsight.com