psm_utils

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

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	psm_utils tag	Read support	Write support	Comments
AlphaDIA precursors TSV	alphadia	✅	❌
CBOR	cbor	✅	✅	Requires the optional cbor2 dependency (pip install psm-utils[cbor])
DIA-NN TSV	diann	✅	❌
DIA-NN report.parquet	diann_parquet	✅	❌
FlashLFQ generic TSV	flashlfq	✅	✅
FragPipe PSM TSV	fragpipe	✅	❌
ionbot CSV	ionbot	✅	❌
JSON	json	✅	✅
OpenMS idXML	idxml	✅	✅	Requires the optional openms dependency (pip install psm-utils[idxml])
MaxQuant msms.txt	msms	✅	❌
MS Amanda CSV	msamanda	✅	❌
mzIdentML	mzid	✅	✅
Parquet	parquet	✅	✅
Peptide Record	peprec	✅	✅
pepXML	pepxml	✅	❌
Percolator tab	percolator	✅	✅
Proteome Discoverer MSF	proteome_discoverer	✅	❌
Sage Parquet	sage_parquet	✅	❌
Sage TSV	sage_tsv	✅	❌
ProteoScape Parquet	proteoscape	✅	❌
TSV	tsv	✅	✅
X!Tandem XML	xtandem	✅	❌

Legend: ✅ Supported, ❌ Unsupported

psm_utils online

psm_utils online is a Streamlit-based web server built on top of the psm_utils Python package. It allows you to easily retrieve proteomics PSM statistics for any supported PSM file type, and to convert search engine results from one PSM file format into another. Click the badge above to get started!

Installation

pip install psm-utils

conda install -c bioconda psm-utils

Full documentation

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

Citation

If you use psm_utils for your research, please cite the following publication:

psm_utils: A high-level Python API for parsing and handling peptide-spectrum-matches and proteomics search results.

Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens.

Journal of Proteome Research (2022). doi:10.1021/acs.jproteome.2c00609