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:

The interface is divided into three main sections:

Tab Structure

• Home: Main dashboard and overview
• Configuration: Analysis configuration with the following sub-tabs:
  • Input: Configure input files (MS data, FASTA/Library) and output directory
  • General: Basic configuration options
  • Library: Library specific settings
  • Search: False Discovery Rate and search mode parameters
  • Output: Output report related settings
• ETC: Additional features with the following tabs:
  • Templates: Save, export, and import configuration presets
  • Recent Runs: View analysis progress, history, and queued tasks
  • Queue: Create and manage analysis queues, monitor queue progress

Configuration Indicators

• Red exclamation mark (!): Settings required for this section
• Green checkmark (✓): Settings completed for this section

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 “REVIEW & RUN”

Note: If you see a red exclamation mark in the area highlighted by the blue rounded rectangle, it means the analysis is not ready to run. Ensure all required configurations are completed (indicated by green checkmarks in the Configuration tabs).

Using the Queue Feature

SynapSpec’s queue feature allows you to configure and schedule multiple analyses to run sequentially without manual intervention. Once queued, all tasks will execute automatically in order, freeing you from monitoring each individual analysis.

Accessing the Queue Tab

Navigate to the Queue tab (highlighted in the blue box) to access the queueing functionality. Click the ADD TO QUEUE button in the upper right corner to create a new queue entry.

Configuring a Queue Entry

Configure the queue settings shown in the blue boxes sequentially:

1. Set your desired configuration parameters
2. Click ADD TO QUEUE in the lower right corner to add this configuration to the queue

Running the Queue

Once you have added multiple analyses to the queue (as shown in the orange box), click START QUEUE at the bottom to begin execution. All queued analysis tasks will run automatically in sequence—no need to manually start each one.

Glycoproteomic Analysis

SynapSpec supports glycoproteomic analysis through the Search Mode setting in the Search tab. By switching the search mode, you can perform N-glycopeptide identification in addition to conventional proteomics analysis.

Enabling Glyco Proteomics Mode

Navigate to the Configuration → Search tab and locate the Search Mode dropdown.

Two modes are available:

Mode	Description
Conventional	Standard proteomics search (default)
Glyco Proteomics	Enables N-glycopeptide identification

Note: Currently, only N-glycosylation is supported. O-glyco and other glycan types are not available.

Select Glyco Proteomics to activate the N-Glyco configuration panel.

N-Glyco Configuration

When Glyco Proteomics mode is selected, an N-Glyco Configuration panel expands below the Search Mode selector with the following settings:

Allowed Precursor Charges

Specifies which precursor charge states are considered during glycopeptide identification.

• Select one or more charge values from 1 to 10
• Default: 3, 4, 5, 6, 7
• Multiple values can be selected simultaneously (displayed as chips)
• Glycopeptides typically carry higher charge states than regular peptides due to their larger molecular weight; adjust this range based on your experimental conditions

Max Missed Cleavages

Sets the maximum number of missed tryptic cleavage sites allowed for glycopeptide candidates.

• Accepts integer values of 0 or greater
• Default: 2
• This setting is independent of the missed cleavages setting in the Library tab, which applies only to conventional search

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Output Results

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