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Common utilities for parsing and handling peptide-spectrum matches and search engine results.

Project description

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python.

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About

Introduction

psm_utils is a Python package with utilities for parsing and handling peptide-spectrum matches (PSMs) and proteomics search engine results. It is mainly developed to be used in Python packages developed at CompOmics, such as MS²PIP, DeepLC, and MS²Rescore, but can be useful to anyone dealing with PSMs and PSM files. Moreover, it provides an easy-to-use CLI and web server to convert search engine results from one PSM file format into another.

Goals and non-goals

  • To provide an easy-to-use Python API for handling PSMs.

  • To provide a unified Python API to the plethora of proteomics search engine output formats that are in existence.

  • To follow community standards: psm_utils pragmatically adheres to the standards developed by the HUPO Proteomics Standards Initiative, such as ProForma 2.0 , the Universal Spectrum Identifier, and mzIdentML

  • To be open and dynamic: psm_utils is fully open source, under the permissive Apache 2.0 license. New reader and writer modules can easily be added, and we welcome everyone to contribute to the project. See Contributing for more information.

  • NOT to reinvent the wheel: Instead, psm_utils heavily makes use of packages such as pyteomics and psims that have existing functionality for reading and/or writing PSM files. psm_utils.io provides a unified, higher level Python API build on top of these packages.

Supported file formats

File format

Read support

Write support

OpenMS idXML

MaxQuant msms.txt

MS Amanda CSV

🔧

mzIdentML

🔧

Peptide Record

Percolator tab

TSV

X!Tandem XML

Legend: ✅ Supported, ❌ Unsupported, 🔧 Work in progress

Installation

Install with pip:

pip install psm-utils

Note: In the PyPI package name, a hyphen is used instead of an underscore, as per PEP8 convention.

Full documentation

The full documentation, including a quickstart guide and Python API reference is available on psm_utils.readthedocs.io.

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