Quick Start

Get up and running with SynapSpec in 5 minutes

Quick Start Guide

This guide will get you analyzing mass spectra with SynapSpec in just a few minutes.

Prerequisites

Make sure you have SynapSpec installed before continuing.

Your First Analysis

Option 1: Using the GUI

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

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

  1. Once the GUI opens, navigate to the Input tab and configure the following settings:

    1. Input File (Required): Select your mass spectrometry data file (.raw or .mzML)
    2. Fasta File (Optional): Select a FASTA file for protein sequence database search
      • Note: Either Fasta File or Library File should be provided
    3. Library File (Optional): Select a spectral library file (.tsv or .txt) for library search
      • Note: Either Fasta File or Library File should be provided
    4. Output Directory (Required): Choose where to save the analysis results
  2. After configuration: Review and adjust additional settings in other tabs:
    • General: Basic configuration options
    • Library: Library-specific settings
    • FDR: False Discovery Rate parameters
    • Search Output: Output report related settings
  3. Click “Run Process” to start the analysis
  4. Results will be automatically exported to the output directory in your configured format (CSV, TSV, or Parquet)

Option 2: Using the CLI

Create a basic configuration yaml file:

ms_files:
  - sample_raw_file.raw
general:
  run_mbr: false
  use_hardware_acceleration: false

library:
  library_file: your_library.ddb
  fasta_files:
    - human.fasta
    - contaminants.fasta
  enzyme: trypsin/p
  fixed_modifications: Carbamidomethyl@C
  variable_modification: Oxidation@M;Acetyl@Protein_N-term
  missed_cleavages: 1
  precursor_length_range: [7, 35]
  precursor_charge_range: [2, 4]
  fragment_types: b;y

fdr:
  fdr: 0.01
  keep_decoys: false

output_directory: output

search_output:
  min_correlation: 0.9
  file_format: tsv
  peptide_level_lfq: false
  precursor_level_lfq: false

Run the analysis:

synapspec run config.yaml

Note: For detailed CLI installation and usage instructions for each platform, see the CLI Tutorial.

Result Files

  • pg.matrix: Protein group quantification matrix containing abundance values across samples
  • stats: Statistical analysis results including precursors, proteins, ms1, ms2 errors
  • precursor: Precursor level ion identification and quantification data
  • fragment: Fragment level ion information and matching scores

All files are available in your chosen format (CSV, TSV, or Parquet) as configured in the Search Output tab.