CLI Tutorial

Complete command-line interface reference for SynapSpec

Installation & Running CLI

Linux

Extract the tar archive and run:

./synapspec [COMMAND] [OPTIONS] [ARGUMENTS]

macOS

After installation, run from the terminal:

/Applications/SynapSpec.app/Contents/MacOS/synapspec [COMMAND] [OPTIONS] [ARGUMENTS]

Or add an alias to your shell profile for convenience:

alias synapspec='/Applications/SynapSpec.app/Contents/MacOS/synapspec'

Windows

Note: CLI is not supported on Windows. Please use the GUI application instead.

Global Options

These options work with all commands:

Option Description Default
run Configuration file path -
--no-track Disable user action tracking false

Core Commands

synapspec run

Run mass spectrum analysis with configuration file.

Usage:

synapspec run [CONFIG_FILE]

Arguments:

  • CONFIG_FILE: YAML configuration file path (default: config.yaml)

Configuration File Format

SynapSpec uses YAML configuration files:

Basic Configuration

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_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

Configuration Parameters

ms_files

List of RAW files to be analyzed. Currently, only DIA (Data-Independent Acquisition) files are supported.

Multiple files can be specified

output_directory

Specifies the directory where all result files will be saved.

If the directory does not exist, it will be created automatically.

general

General analysis settings.

  • run_mbr: Enables or disables Match-between-runs (MBR). This feature aligns and transfers features across runs.
  • use_hardware_acceleration: Enables GPU acceleration for improved processing performance. Requires a CUDA-compatible GPU. Note: macOS is not supported.
library

Spectral library configuration.

You can either provide an existing library file or generate an in-silico library from FASTA files.

  • library_file: Path to the spectral library file. This field is required when generate is set to false. Currently, only the MaxQuant format is supported, with plans to support additional formats in the future.
  • fasta_files: List of FASTA files used for generating an in-silico library. Required when generate is true.
  • enzyme: Digestion enzyme used for peptide generation, e.g. trypsin/p.
  • fixed_modifications: Fixed modifications applied during digestion, e.g. Carbamidomethyl@C.
  • variable_modification: Variable modifications; multiple entries can be separated by semicolons (;), e.g. Oxidation@M;Acetyl@Protein_N-term.
  • missed_cleavages: Number of allowed missed cleavages.
  • precursor_length_range: Range of peptide lengths to include, e.g. [7, 35].
  • precursor_charge_range: Range of precursor charge states to include, e.g. [2, 4].
  • fragment_types: Fragment ion types to use, e.g. b;y.

When library_file is specified, digestion and modification options are ignored.

When generate is true, you must specify fasta_files, and library_file is not required.

fdr

False Discovery Rate (FDR) configuration.

  • fdr: FDR threshold. Typically set to 0.01 (1%).
  • keep_decoys: Determines whether decoy entries are retained in the final output.
output

Search result and output format configuration.

  • min_correlation: Minimum correlation between fragments used for quantification. Fragments with correlation below this threshold will be excluded.
  • file_format: Output file format, e.g. tsv.
  • peptide_level_lfq: Enables peptide-level LFQ quantification.
  • precursor_level_lfq: Enables precursor-level LFQ quantification.

Summary

  • When library.generate: true, fasta_files must be provided.
  • When library.generate: false, library_file must be provided.
  • Other settings under library (e.g. enzyme, modifications, charge range) apply only when generating an in-silico library.