MZmine 3 Documentation
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MZmine 3 Documentation
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Processing wizard
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Processing modules
Processing modules
I/O
I/O
Raw data import
Raw data export
Feature list import
Feature list export
Export to other software
Spectral library export
File merging
File merging
Raw data files merging
Mobility scan merging
Raw data filtering
Raw data filtering
Scan by scan filtering
Crop filter
Baseline corrections
Align scans
Scan smoothing
Mass detection
Mass detection
Mass detection
Mass detection algorithms
FTMS shoulder peak finder
Mass calibration
LC-MS feature detection
LC-MS feature detection
ADAP Chromatogram builder
GridMass
Targeted feature detection
Feature detection results
LC-IMS-MS feature detection
LC-IMS-MS feature detection
Ion mobility expander
Ion mobility trace builder
Recursive IMS builder
MS imaging feature detection
MS imaging feature detection
Image builder
Smoothing
Resolving
Resolving
Local minimum resolver
ADAP resolver
Baseline resolver
CentWave resolver
Noise amplitude resolver
Savitzky-Golay resolver
Spectral deconvolution (GC)
Spectral deconvolution (GC)
Hierarchical clustering
Multivariate curve resolution
CCS calibration
MS2 scan pairing
MALDI MS2 scan pairing (SIMSEF)
Isotope filtering
Isotope filtering
13C isotope filter (isotope grouper)
Isotope pattern finder
Isotope peak scanner
Feature grouping
Feature grouping
Correlation grouping
Ion identity networking
Feature list filtering
Feature list filtering
Duplicate feature filter
Feature list rows filter
Feature filter
Peak comparison rows filter
Neutral loss filter
m/z mobility region extraction
Feature list blank subtraction
Alignment
Alignment
Join aligner
Merge lists
RANSAC aligner
Hierachical aligner (GC)
ADAP aligner (GC)
LC Image Aligner
Gap filling
Gap filling
Peak finder
Same RT and m/z range gap filler
Normalization
Normalization
Retention time calibration
Linear normalizer
Standard compound normalizer
Precursor mass search
Precursor mass search
Local database search
Precursor search in local spectral MS/MS library
Online compound database search
Spectra search
Spectra search
Spectral library search
NIST MS search
Chemical formula prediction
Lipid annotation
MS2 similarity search
Other parameters
Other parameters
Merge MS/MS
Spectra similarity
Visualization modules
Visualization modules
Visualization overview
MS data visualisation
MS data visualisation
Raw data overview
Additional tools
Ion mobility data visualisation
Image viewer
Image co-localization
Processed data visualition
Processed data visualition
MSMS Visualizer
Interactive Ion Identity Molecular Networks
Feature histograms
Additional tools
Massvoltammogram
Workflows
Workflows
Untargeted LC-MS workflow
Untargeted LC-IMS-MS workflow
Untargeted MS imaging workflow
Batch processing
Library generation
SIMSEF
Tools
Tools
SIMSEF scheduler
Additional resources
Additional resources
General Terminology
IMS Terminology
LC-MS and LC-IMS-MS data comparison
Kendrick mass defect
Spectral similarity measures
Contribute
Contribute
Coding
Coding
MZmine development (in IntelliJ)
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General structure
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Module development
Modules list
Contribute to documentation
Documentation template
Acknowledgements
Troubleshooting
Changelog
Workshops
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