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SynapSpecv0.12.1

Welcome to SynapSpec

Latest version: v0.12.1 · Release Notes

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

Section titled “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.

Terminal window
synapspec run config.yaml

CLI Tutorial →

Core Features

Section titled “Core Features”

Peptide Identification & Quantification

Section titled “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

Section titled “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

Section titled “Label-free Quantification”

Support for both label-free and isobaric labeling method for multiplexed quantitative proteomics experiments.

DIA Analysis

Section titled “DIA Analysis”

Optimized workflows for data-independent acquisition and SWATH-MS analysis with spectral library generation and matching.

Statistical Analysis & Differential Expression

Section titled “Statistical Analysis & Differential Expression”

Integrated statistical tools for differential expression analysis and multiple testing correction.

Supported Formats

Section titled “Supported Formats”

Input Formats:

  • .raw
  • .d
  • .mzML

Library Formats:

  • .txt (MaxQuant format)
  • .tsv (MaxQuant format)

Output Formats:

  • .csv
  • .tsv
  • .parquet

Installation

Section titled “Installation”

Get started with SynapSpec in minutes. View detailed installation guide →

Section titled “Popular Documentation”
Quick Start GuideGet up and running in 5 minutes
GUI TutorialInteractive analysis with graphical interface
CLI TutorialCommand-line tools for batch processing
Community SupportGet help and connect with other users

Need Help?

Section titled “Need Help?”