Documentation

SPLAT enables simultaneous protein localization and turnover analysis from mass spectrometry-based proteomics experiments.

Author

Edward Lau

Published

March 30, 2023

Abstract

This page provides the documentation for the SPLAT package, which is a tool for simultaneously measuring the spatial and temporal dynamics of proteins in the cell.

Installation

The splat-workflow package can be installed via pip and will automatically install the dependencies of splat. After installation, the splat command will be available in your path.

Dependencies

Installing splat-workflow will automatically install the following dependencies:

riana==0.7.1
pytmt=0.4.1

In addition, SPLAT requires the following software to be installed to analyze mass spectrometry files:

Comet
Percolator

Usage

To run SPLAT, edit the YAML configuration file inside the config directory, then run Snakemake.

snakemake --configfile config/config.yaml -c

An example configuration file is provided in the config directory.

# Config

# Data location. Add as many lines as needed, sample names should be named after
# labeling time points (e.g., time12 for 12 days/12 hours of experiment)
data:
  time0: /path/to/time0/folder
  time1: /path/to/time1/folder
  time3: /path/to/time3/folder
  time6: /path/to/time6/folder

# Paths to the comet executable, the comet params file, the database, and the percolator executable
# The Snakefile assumes riana can be executed in the shell by riana
paths:
  comet: /path/to/comet_source_2020013/comet.exe
  comet_params: /path/to/params/comet.params
  fasta: /path/tp/database.fas
  percolator: /path/to/percolator

# Integration and fitting parameters
params:

  # riana integrate parameters
  isotopomers: 0,1,2,3,4,5   # isotopomer to integrate (0,1,2,3,4,5 for deuterium; 0,6 for heavy aa)
  mass_tol: 15         # mass tolerance in ppm for integration (e.g., 25)
  ria_max: 1          # final precursor ria
  depth: 1             # minimum number of data points
  aa: K                 # which amino acid carries heavy label; only relevant if label_type is aa
  mass_defect: D        # which isotope mass defect to use (D, C13, SILAC)

  # riana fitcurve parameters
  model: simple     # fitting model (simple, guan, fornasiero)
  label_type: hw        # labeling type (aa or hw)
  kp: 10              # guan model parameter (kp) or fornasiero model parameter (b)
  kr: 0.15              # fornasiero model parameter (a)
  rp: 5.52              # fornasiero model parameter (r)

  # pytmt parameters
  multiplexity: 10
  contaminants: /path/to/contaminants.txt

# Number of threads
threads:
  comet: 8
  riana: 4
  fitcurve: 12

All options

python -m splat -h
usage: __main__.py [-h] [-t TMT [TMT ...]] [-o OUTPUT] [-v] SILAC

SPLAT: Simultaneous Proteome Localization and Turnover

positional arguments:
  SILAC                 SILAC input file

optional arguments:
  -h, --help            show this help message and exit
  -t TMT [TMT ...], --tmt TMT [TMT ...]
                        TMT input file(s) (default: None)
  -o OUTPUT, --output OUTPUT
                        output file path (default: splat_output.txt)
  -v, --version         show program's version number and exit

For more information, see GitHub repository at https://github.com/lau-lab/splat