Infrastructure

Built for mass spectrometry, powered by open source.

OpenMS-lib is the BSD-licensed C++ foundation behind TOPP tools, pyOpenMS, and community software—for LC-MS data management, analysis, and visualization.

BSD-3 license
C++ & Python
Cross-platform
200+ TOPP tools

C++ documentation pyOpenMS Build from source

At a glance

Core library & ecosystem

One C++ core powers command-line tools, Python bindings, and community web apps.

Core library

C++ algorithms & data structures

File I/O for mzML, mzXML, TraML, mzIdentML, and related formats, plus signal processing, identification, and quantification building blocks.

Modular, extensible C++ API
Cross-platform (Windows, macOS, Linux)
Three-clause BSD license

Ecosystem

Built on OpenMS-lib

Most users interact with OpenMS through tools and bindings that share the same core.

TOPP tools — command-line utilities
pyOpenMS — Python bindings
Web apps — community projects

Source on GitHub

BSD licensed

Open source

Core library and tools you can extend, share, and ship under a three-clause BSD license.
C++ Python

C++ & Python

High-performance algorithms with pyOpenMS for scripting and workflows.
Windows macOS Linux

Cross-platform

Build and run on all major platforms with the same toolchain.
200+ tools

TOPP pipeline

Ready-made command-line utilities for proteomics and metabolomics analysis.

KNIME

Run existing workflows

Use OpenMS workflows for proteomics and metabolomics in KNIME without writing code.
KNIME guide
Galaxy

Create your own workflows

Modify and compose OpenMS workflows across Galaxy, KNIME, and Nextflow.
Workflow guide
pyOpenMS

Use OpenMS in Python

Extend pipelines with pyOpenMS scripts or prototype new analysis methods in Python.
pyOpenMS docs

Nextflow

Analyze large datasets

Run workflows on very large datasets on powerful compute infrastructure.
Nextflow guide
$

Progress of 'loading spectra list':
-- done [took 0.19 s (CPU), 0.19 s (Wall)] --

Memory usage (loading MS data): 25 MB (working set delta), 25 MB (peak working set delta)

-- General information --

File name: example.mzML
File type: mzML

Instrument: LTQ Orbitrap XL
  Mass Analyzer: Orbitrap (resolution: 0)

MS levels: 1, 2
Total number of peaks: 479455
Number of spectra: 1684

Ranges:
  retention time: 1501.41 .. 2499.52 sec (16.6 min)
  mass-to-charge: 85.81 .. 799.95
  intensity: 0.67 .. 11977811.00

Number of spectra per MS level:
  level 1: 564
  level 2: 1120

Peak type from metadata (or estimated from data)
  level 1: Centroid (Centroid)
  level 2: Centroid (Centroid)

Activation methods
  MS-Level 2 & CID (Collision-induced dissociation): 1120

Precursor charge distribution:
  charge 2: 679x
  charge 3: 399x
  charge 4: 33x
  charge 5: 8x
  charge 6: 1x

FileInfo took 0.26 s (wall), 0.26 s (CPU), 0.01 s (system), 0.25 s (user); Peak Memory Usage: 59 MB.

C++ / OpenMS

Create high-performance tools

Develop high-performance tools or algorithms with the C++ OpenMS library.
C++ tutorial