The open-source framework for Mass Spectrometry
OpenMS developers meeting 17-21 March 2025, in Xewkija, Gozo, Malta
2024-12-19

What is OpenMS ?

OpenMS offers an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization. It empowers rapid development of mass spectrometry related software. OpenMS is freely available under the three clause BSD license and runs under Windows, macOS and Linux. The OpenMS members have a strong commitment to creating an open, inclusive, and positive community. Please read the OpenMS Code of Conduct for guidance on how to interact with others in a way that makes the community thrive.

New: WebApps

This app offers the powerful UmetaFlow pipeline for untargeted metabolomics in an accessible user interface.

NuXL is a dedicated software package designed for the analysis of XL-MS (cross-linking mass spectrometry)...

NASEWEIS is webapp version of the NucleicAcidSearch
Engine, it is a tool to do library searching of Oligonucleotide

FLASHTaggerviewer visualize output from FLASH* tools. FLASH* tools can deconvolute your Topdown data very...

Sage search engine is a fast and reliable proteomics search engine for the anaylsis of MS data...

OpenMS allows users to:

Description

Run existing workflows

Run existing workflows for proteomics and metabolomics with OpenMS in KNIME.

Create your own workflows

Modify and create your own OpenMS workflows in Galaxy, KNIME and Nextflow.

Description
Description

Use OpenMS in Python

Enhance workflows with pyOpenMS scripts or develop novel methods using pyOpenMS


Advanced users / developers can use OpenMS to:

Description

Analyze large datasets

Run workflows on very large datasets on powerful compute infrastructure

Create high-performance tools

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

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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.

Quick facts for Users...