Launching the GUI

Launch the graphical interface by double-clicking the SynapSpec application icon:

• Linux: Double-click SynapSpec in Applications folder
• macOS: Double-click SynapSpec in Applications folder
• Windows: Double-click SynapSpec.exe in the installation folder

Interface Overview

Main Window Layout

The GUI is organized with a tab-based interface:

Tab Structure

• Input: Configure input files (MS data, FASTA/Library) and output directory
• General: Basic configuration options
• Library: Library specific settings
• FDR: False Discovery Rate parameters
• Search Output: Output report related settings
• Log: View real-time processing logs

Control Elements

• Run Process Button: Located at the bottom to start analysis
• Status Indicator: Located in the upper right corner, displays current process status

Loading Data

Supported File Types

• Raw Files: .raw, .mzML
• Fasta Files: .fasta
• Library Files: .tsv, .txt
• Output formats: .csv, .tsv, .parquet

Configuring Input Settings

Navigate to the Input tab and configure the following:

Step 1: Input Files - Click Select Input Files to choose your mass spectrometry data (.raw or .mzML)

Step 2: FASTA or Library File (choose one)

• Click Select Fasta Files for protein sequence database search, OR
• Click Select Library File for spectral library search (.tsv or .txt)

Step 3: Output Directory - Click Select Output Directory to choose where results will be saved

Step 4: Click “Run Process”

Output Results

After the analysis completes, SynapSpec generates the following output files in your specified output directory