Summary

pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python. pyOpenMS implements a set of Python bindings to the OpenMS library for computational mass spectrometry and is available for Windows, Linux and macOS.

pyOpenMS provides functionality that is commonly used in computational mass spectrometry. The pyOpenMS package contains Python bindings for a large part of the OpenMS library for mass spectrometry based proteomics. It thus provides easy access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis.

pyOpenMS facilitates the execution of common tasks in proteomics (and other fields of mass spectrometry) such as

• File handling (mzXML, mzML, TraML, mzTab, FASTA, pepxml, protxml, mzIdentML among others)

• Chemistry (mass calculation, peptide fragmentation, isotopic abundances)

• Signal processing (smoothing, filtering, de-isotoping, retention time correction and peak-picking)

• Identification analysis (including peptide search, PTM analysis, cross-linked analytes, FDR control, RNA oligonucleotide search and small molecule search tools)

• Quantitative analysis (including label-free, metabolomics, SILAC, iTRAQ and SWATH/DIA analysis tools)

• Chromatogram analysis (chromatographic peak picking, smoothing, elution profiles and peak scoring for SRM/MRM/PRM/SWATH/DIA data)

• Interaction with common tools in proteomics and metabolomics:

  • Search engines such as Comet, Mascot, MSGF+, MSFragger, SpectraST, Sage

  • Post-processing tools such as Percolator, MSstats, Epiphany

  • Metabolomics tools such as SIRIUS, CSI:FingerId

User Guide

Information about installing and using pyopenms.

• User guide
  • Introduction
  • Why use OpenMS
  • Liquid chromatography (LC)
  • Mass Spectrometry (MS)
  • Identification and Quantification of Ions
  • Installation
  • Import pyOpenMS
  • Using the Help Function
  • First Look at Data
  • MS Data
  • Chemistry
  • Peptides and Proteins
  • Oligonucleotides: RNA
  • Fragment Spectrum Generation
  • Spectrum Alignment
  • Digestion
  • Identification Data
  • Quantitative Data
  • Parameter Handling
  • Algorithms
  • Smoothing
  • Centroiding
  • Spectrum Normalization
  • Spectra Merge Algorithm
  • Charge and Isotope Deconvolution
  • Feature Detection
  • Map Alignment
  • Adduct Detection
  • Feature Linking
  • Peptide Search
  • Chromatographic Analysis
  • Quality Control
  • Mass Decomposition
  • Export Files for GNPS
  • Identification by Accurate Mass
  • Untargeted Metabolomics Pre-Processing
  • Logging
  • Reading Raw MS Data
  • Other MS Data Formats
  • mzML Files
  • Scoring Spectra
  • Export to pandas DataFrame
  • Query MSExperiment with MassQL
  • Memory Management
  • pyOpenMS in R
  • Interactive Plots
  • Interfacing with ML Libraries
  • Support
  • Frequently Asked Questions
  • OpenMS Glossary
• Indices and Tables

API documentation

Documentation on modules, functions, classes of this package.

• API docs
  • pyopenms
  • pyopenms.Constants
  • pyopenms.plotting

Community and contribution guide

Information about the community behind this package and how you can contribute.

• Contribute
  • pyopenms docs
  • pyopenms sources