metabolomics software tools - university of alabama at …€¦ · · 2015-06-17• software...
TRANSCRIPT
Metabolomics Software Tools
Xiuxia Du, Paul Benton, Stephen Barnes
Outline
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• Introduction !!
• Software Tools for LC-MS metabolomics !
!• Software Tools for GC-MS metabolomics !
!• Software Tools for Statistical Analysis !!!!!!!
• LC-MS data analysis workflow !!!!!!!!
!• GC-MS data analysis workflow !!!!
Introduction
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data pre- processing
statistical analysis
compound identification
pathway analysis
feature extraction
statistical analysis
compound identification
pathway analysis
deconvolution
Software Tools for LC-MS
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• Commercial
• MassHunter — Agilent • MetQuest — Thermo Scientific • MetWorks — Thermo Scientific • Multiple Mass Defect Filter — Thermo Scientific • Progenesis QI — Waters • XCMSplus — Sciex
!!• and more ……
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Software Tools for LC-MS
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• Free • Insilicos Viewer !
• ProteoWizard
• SeeMS: interactive viewer for mass spec data files (Windows only)
• MSConvert: convert between various file formats
!• MZmine 2: LC-MS data processing
!• MetaboSearch: perform mass-based metabolite search simultaneously
against four major metabolite databases !
• MetaboAnalyst: a web server for metabolomics data analysis
!• and more ……
• Proprietary data formats: need vendor library functions to access !!!!!!!!!• Open data formats: free library functions to access
• netCDF • mzData • mzXML • mzML
Data format
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Company File extension
Agilent .D
Sciex .WIFF
Theomo .RAW
Waters .RAW
……
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InsilicosViewer
Insilicos Viewer
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Raw data viewer
total ion chromatogram
MS and MS/MS
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ProteoWizard
ProteoWizard: SeeMS
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• A data viewer
!!!!• Can read these open data formats
• mzML • mzXML !!
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ProteoWizard: SeeMS
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Raw data viewer
total ion chromatogram
spectrum
list of scans
ProteoWizard: MSConvert
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Data format converter
ProteoWizard: MSConvert
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• Supported data formats
• Read: open formats, vendor formats • Write: open formats
!• Filters and transformation
• msLevel • Peak picking • Zero samples • ETD filter • Threshold peak filter • Charge state predictor • Activation • Subset !!
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MZmine 2
MZmine 2
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• LC-MS metabolomics data processing, analysis, and visualization !!!!!!• Supported open data formats
• NetCDF • mzData • mzML • mzXML
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Raw data import
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list of scans in raw files • MS scans in blue • MS/MS scans in red • # sequential number • @ retention time • MS level • type of spectrum
• p = profile • c = centroid • t = thresholded
• polarity of ionization • + = positive • - = negative • ? = unknown
Raw data visualization
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Right click on the file name
brings up
Raw data visualization
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total ion chromatogram
spectrum
double click TIC
brings up
Raw data visualization
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2D view
Raw data visualization
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3D view
rotate to find the best perspective
Data pocessing
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• Workflow
• Raw data import • (optional) Raw data methods / Filtering • Peak detection • Isotopic peak grouping • (optional) Identification of fragments, adducts, and peak complexes • (optional) Normalization of retention time • Alignment • (optional) Gap filling • (optional) Normalization of peak heights / areas • (optional) Identification using database search, formula prediction, etc. • Data analysis and export !!
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Peak detection
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• Mass detection
• Centroid • Exact mass • Local maxima • Recursive threshold • Wavelet transform
!• Chromatogram building
!• Peak deconvolution
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Peak detection
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Peak detection procedure
Mass detection
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Mass detection options
click
her
e to
brin
g up
the p
aram
eter
win
dow
Mass detection
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Set mass detection parameter
Mass detection
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Set mass detection parameter
Chromatogram building
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Chromatogram builder
Chromatogram building
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Chromatogram builder — set parameters
Chromatogram building
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peak list • # ID • m/z value • @ retention time
After chromatograms are built
Chromatogram building
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To display extracted ion chromatograms
Right click on the file name
brings up
Chromatogram building
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Show chromatogram information
Chromatogram building
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Show chromatogram information
a particular extracted ion chromatogram (EIC)
Peak deconvolution
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Peak deconvolution
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Algorithms
Peak deconvolution
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Set parameters
click hereto bring up the parameter window
Peak deconvolution
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deconvolution finish
ed
Peak deconvolution
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Results
Alignment
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Retention time normalization
Alignment
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Retention time normalization: set parameters
Alignment
Join aligner
Alignment
Join aligner: set parameters
Alignment
Get aligned peak list
Alignment
Information on aligned peak list
Green: present Red: absent
Peak identification
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Options
Peak identification
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By searching custom databases
an example custom database
Peak identification
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By adduct search: set parameters
Peak identification
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Adduct search results
Peak identification
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By online database search
Peak identification
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Online database search results
Gap filling
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Options and parameters
Gap filling
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Results and visualization options
Gap filling
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Set visualization parameters
Gap filling
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Visualization
Data analysis
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Options
Data export
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Options
Data export
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Parameters
Data export
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csv format
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MetaboSearch
MetaboSearch
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Input data format
http://omics.georgetown.edu/metabosearch.html#ug
MetaboSearch
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GUI
MetaboSearch
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Steps
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Software tools for GC-MS Metabolomics
Software Tools for GC-MS
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• Commercial
• ChromaTOF® — LECO • MassHunter — Agilent
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• Free
• AMDIS: Automated Mass Spectral Deconvolution and Identification System
• NIST MS Search
• Tagfinder !!
AMDIS
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Raw data visualization
AMDIS
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Result visualization
NIST MS Search
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GUI
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Software tools for Statistical Analysis
Stats and Machine Learning
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• Commercial
• SIMCA • Mass Profiler Professional (MPP) — Agilent !
• and more …… !!!!!• Free
• MetaboAnalyst
• R !!!
MetaboAnalyst
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Other software tools
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• COMSPARI
• COMparison of SPectral And Retention Information !
• MathDAMP
• Mathematica package for Differential Analysis of Metabolite Profiles !• MSFACTs
• Metabolomics Spectral Formatting, Alignment and Conversion Tools !!and many more …… !!!!!
Thank You!