AlphaSynchro

This package is intended to convert a clusters.hdf file with alphasynchro data into a spectrum file.

Installation

• Steps
  • Download timspeak: git clone https://github.com/MannLabs/timspeak.git
  • Download alphasynchro: git clone https://github.com/MannLabs/alphasynchro.git
  • Create conda env: conda create -n synchro python=3.10 -y
  • Activate: conda activate synchro
  • Install Sage: conda install -c bioconda -c conda-forge sage-proteomics -y
  • Install timspeak and alphasynchro: pip install -e ./timspeak -e ./alphasynchro

Usage

• Required
  • Config folder (e.g. example) containing:
    • timspeak.config
    • sage.config
    • species.fasta
  • raw_data.d
• Usage
  • Copy-paste examplary command-line input in the example folder and modify.
  • Note: if working with regular dia-PASEF rather than synchro-PASEF, use line 15 instead of 14 (add the --diapasef, but furtherwise identical).
  • Run ./example/cmd.sh