Quick Start

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

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. From Home, click New Analysis to open the four-step wizard.

2. Step 1 — Files: select your mass spectrometry data and a sequence database.

   1. MS Files (Required): click Select Input Files and choose your data (.raw or .mzML)
   2. FASTA Files (Optional): select a FASTA file for protein sequence database search
      • Note: Either FASTA Files or Library File should be provided
   3. Library File (Optional): select a spectral library file (.tsv or .txt) for library search
      • Note: Either FASTA Files or Library File should be provided

3. Step 2 — Method: review and adjust the library generation, FDR, and general settings.

4. Step 3 — Output: choose your Output Directory (Required) and the output format (CSV, TSV, or Parquet).

5. Step 4 — Review: check the summary, then click Run Now to start immediately, or Add to Queue to run it after the current analysis.

6. Track progress and results from the Runs page. Results are automatically exported to the output directory in your configured format (CSV, TSV, or Parquet).

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 Output step.