msproteomics 0.1.0

A Python package for mass spectrometry-based proteomics data processing

msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease

This repository contains a Python package to report phosphosites and phosphopeptides from a DIA-MS phosphoproteomics experiment.

Data

• Skowronek et al. PXD034128 dataset
  • Spectronaut 16 output: data/20220530_113551_Phospho_optimal_dia-PASEF_21min_v16_Report.xls
  • DIA-NN 1.8 output: data/Phospho_EGF_diAID.tsv
• Skowronek et al. PXD034128 data re-processsed
  • Spectronaut 18 output: data/20231106_133459_optimal4_Report.tsv
  • DIA-NN 1.8.2 output: data/report.tsv
• Bekker-Jensen et al. PXD014525 dataset re-processed
  • Spectronaut 18 output: olsen-long-format-ptm-report.tsv
  • Spectronaut 18 pivot export: olsen-wide-format-site-report.tsv

Installation

pip install msproteomics

On some system, you might need to install pybind11 first, for example

conda create -n p37 python=3.7
conda activate p37
pip install pybind11
pip install msproteomics

Example usages

For Spectronaut export

sitereport 20231106_133459_optimal4_Report.tsv -tool sn

For DIA-NN export

read_diann -o report_msproteomics.tsv -f uniprot-reviewed_yes_AND_organism__Homo_sapiens__Human___9606___--.fasta report.tsv

sitereport report_msproteomics.tsv