Processing analytical data
Process spectra, extract features and quantify targets.
How to choose a resource
MS measurements need processing before comparison: detect signals, correct or align spectra, and assemble quantitative tables. A feature is not necessarily a single identified metabolite.
Check your acquisition mode and file format, the quality-control steps available, and whether you prefer a graphical or scripted workflow.
Tools & resources
19 entriesMZmine
Free for academic useA modular mass-spectrometry environment for raw-data import, feature detection/alignment, multimodal LC/IMS/GC/MSI processing, molecular networking, annotation, lipid analysis, visualization, normalization, statistics, and downstream exports.
Multimodal feature processingMS-DIAL
Source available with restrictionsA graphical and command-line workbench for untargeted metabolomics and lipidomics data processing across multiple chromatography and mass spectrometry platforms.
Deconvolution & lipid annotationxcms
Open sourceAn open-source Bioconductor package for chromatographic mass spectrometry data preprocessing, feature detection, alignment, grouping, and visualization.
Scripted preprocessing in ROpenMS
Open sourceAn open-source C++ library, command-line toolkit, and Python interface for reproducible mass spectrometry data processing in metabolomics and proteomics.
Custom processing workflowsmsconvert
Open sourceConvert mass-spectrometry files into open formats for downstream analysis.
Convert instrument filesasari
Source available with restrictionsProcess high-resolution mass-spectrometry data into aligned feature tables.
High-resolution feature extractionpatRoon
Open sourceAssemble reproducible non-target screening workflows for environmental mass spectrometry in R.
Environmental non-target workflowsOpenChrom
Open sourceInspect and process chromatographic and mass-spectrometric data in a desktop workbench.
Graphical chromatogram analysisIPO
Open sourceOptimize peak picking, retention-time correction and grouping parameters for XCMS.
Tune XCMS parametersCAMERA
Open sourceGroup and annotate related LC-MS signals after XCMS peak detection.
Group isotopes and adductsRAMClustR
Source available with restrictionsCluster related mass-spectrometry features and export compound-level spectra and abundances.
Cluster compound-related featuresSmartPeak
Open sourceAutomate targeted and semi-targeted chromatographic data processing and quantification.
Targeted peak integrationPeakBot
Source available with restrictionsDetect chromatographic peaks in profile-mode LC-HRMS data using machine learning.
Learned chromatographic peak detectionMSnbase
Open sourceManipulate, process and visualize mass-spectrometry data within R.
R infrastructure for MS dataSpectra
Open sourceStore, filter, process and compare mass spectra through a common R interface.
Scalable spectra objects in RSkyline
Source available with restrictionsDevelop and review targeted mass-spectrometry assays, including small-molecule quantification.
Targeted small-molecule quantificationLipidCreator
Open sourceDesign targeted lipidomics assays and predicted fragment libraries for PRM and MRM experiments.
Data acquisition and instrument controlMSHub-GC
Free web serviceGC-MS processing workflow that aligns chromatographic data and deconvolves overlapping signals into spectra and quantitative tables for downstream GNPS analysis.
GC-MS alignment & deconvolutionpeakPantheR
Open sourceR package for targeted extraction and integration of predefined metabolic features across LC-MS profiling files.
Extract predefined LC-MS feature panels