Research
A curated bibliography of scientific publications that reference OpenMS software, methods, and workflows. Showing publications from the two most recent years. Use the dropdown to switch between them.
When you use OpenMS in your research, please cite the key publications below and the tools you used where applicable. See also the Citing OpenMS page for citation guidance.
Primary references when citing OpenMS software and the Python interface.
A proteomics sample metadata representation for multiomics integration and big data analysis
DIAproteomics: A multifunctional data analysis pipeline for data-independent acquisition proteomics and peptidomics
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy
Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
FLASHDeconv: ultrafast, high-quality feature deconvolution for top-down proteomics
Feature-based molecular networking in the GNPS analysis environment
Metabolomics data processing using OpenMS
OpenPepXL: an open-source tool for sensitive identification of cross-linked peptides in XL-MS
Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells
SmartPeak automates targeted and quantitative metabolomics data processing
Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities
EPIFANY-A method for efficient high-confidence protein inference
MHCquant: automated and reproducible data analysis for immunopeptidomics
Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma
Recommendations for the packaging and containerizing of bioinformatics software
ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion
Automated SWATH data analysis using targeted extraction of ion chromatograms
BioContainers: an open-source and community-driven framework for software standardization
OpenMS–a platform for reproducible analysis of mass spectrometry data
Targeted feature detection for data-dependent shotgun proteomics
The mzIdentML data standard version 1.2, supporting advances in proteome informatics
A multicenter study benchmarks software tools for label-free proteome quantification
Flexible data analysis pipeline for high-confidence proteogenomics
OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Ten simple rules for taking advantage of Git and GitHub
Efficient visualization of high-throughput targeted proteomics experiments: TAPIR
Fast and efficient XML data access for next-generation mass spectrometry
Retention time prediction improves identification in nontargeted lipidomics approaches
Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling
Workflows for automated downstream data analysis and visualization in large‐scale computational mass spectrometry
Automated label-free quantification of metabolites from liquid chromatography–mass spectrometry data
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
qcML: an exchange format for quality control metrics from mass spectrometry experiments
An automated pipeline for high-throughput label-free quantitative proteomics
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics
Tools for label-free peptide quantification
TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data
The mzIdentML data standard for mass spectrometry-based proteomics results
OpenMS and TOPP: open source software for LC-MS data analysis
Probabilistic consensus scoring improves tandem mass spectrometry peptide identification
Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics
TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation
OpenMS and TOPP: open source software for LC-MS data analysis
SILACAnalyzer-a tool for differential quantitation of stable isotope derived data
Analysis of mass spectrometric data: peak picking and map alignment
Computational quantification of peptides from LC-MS data
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
LC-MSsim–a simulation software for liquid chromatography mass spectrometry data
OpenMS–an open-source software framework for mass spectrometry
A fast and accurate algorithm for the quantification of peptides from mass spectrometry data
A geometric approach for the alignment of liquid chromatography—mass spectrometry data
TOPP The OpenMS Proteomics Pipeline
Absolute quantification of myoglobin content in blood serum using HPLC/MS through automatic bioinformatics analysis
Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples
OPENMS; a generic open source framework for chromatography/MS-based proteomics
OpenMS-Software for Mass Spectrometry