Metabolomics Software Tools Xiuxia Du, Paul Benton, Stephen Barnes
Outline 2 Introduction Software Tools for LC-MS metabolomics Software Tools for GC-MS metabolomics Software Tools for Statistical Analysis
Introduction LC-MS data analysis workflow GC-MS data analysis workflow data preprocessing feature extraction statistical analysis deconvolution statistical analysis compound identification compound identification pathway analysis pathway analysis 3
Software Tools for LC-MS Commercial MassHunter Agilent MetQuest Thermo Scientific MetWorks Thermo Scientific Multiple Mass Defect Filter Thermo Scientific Progenesis QI Waters XCMS plus Sciex and more 4
Software Tools for LC-MS 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 5
Data format Proprietary data formats: need vendor library functions to access Open data formats: free library functions to access netcdf mzdata mzxml mzml Company File extension Agilent.D Sciex Theomo Waters.WIFF.RAW.RAW 6
InsilicosViewer 7
Insilicos Viewer Raw data viewer total ion chromatogram MS and MS/MS 8
ProteoWizard 9
ProteoWizard: SeeMS A data viewer Can read these open data formats mzml mzxml 10
ProteoWizard: SeeMS Raw data viewer total ion chromatogram spectrum list of scans 11
ProteoWizard: MSConvert Data format converter 12
ProteoWizard: MSConvert 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 13
MZmine 2 14
MZmine 2 LC-MS metabolomics data processing, analysis, and visualization Supported open data formats NetCDF mzdata mzml mzxml 15
Raw data import 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 16
Raw data visualization brings up Right click on the file name 17
Raw data visualization double click TIC total ion chromatogram brings up spectrum 18
Raw data visualization 2D view 19
Raw data visualization rotate to find the best perspective 3D view 20
Data pocessing 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 21
Peak detection Mass detection Centroid Exact mass Local maxima Recursive threshold Wavelet transform Chromatogram building Peak deconvolution 22
Peak detection Peak detection procedure 23
Mass detection Mass detection options click here to bring up the parameter window 24
Mass detection Set mass detection parameter 25
Mass detection Set mass detection parameter 26
Chromatogram building Chromatogram builder 27
Chromatogram building Chromatogram builder set parameters 28
Chromatogram building After chromatograms are built peak list # ID m/z value @ retention time 29
Chromatogram building To display extracted ion chromatograms brings up Right click on the file name 30
Chromatogram building Show chromatogram information 31
Chromatogram building Show chromatogram information a particular extracted ion chromatogram (EIC) 32
Peak deconvolution 33
Peak deconvolution Algorithms 34
Peak deconvolution Set parameters click here to bring up the parameter window 35
Peak deconvolution deconvolution finished 36
Peak deconvolution Results 37
Alignment Retention time normalization 38
Alignment Retention time normalization: set parameters
Join aligner Alignment
Join aligner: set parameters Alignment
Get aligned peak list Alignment
Alignment Information on aligned peak list Green: present Red: absent
Peak identification Options 44
Peak identification By searching custom databases an example custom database 45
Peak identification By adduct search: set parameters 46
Adduct search results Peak identification 47
By online database search Peak identification 48
Peak identification Online database search results 49
Options and parameters Gap filling 50
Gap filling Results and visualization options 51
Set visualization parameters Gap filling 52
Gap filling Visualization 53
Data analysis Options 54
Data export Options 55
Data export Parameters 56
Data export csv format 57
MetaboSearch 58
MetaboSearch Input data format 59 http://omics.georgetown.edu/metabosearch.html#ug
MetaboSearch GUI 60
MetaboSearch Steps 61
Software tools for GC-MS Metabolomics 62
Software Tools for GC-MS Commercial ChromaTOF LECO MassHunter Agilent Free AMDIS: Automated Mass Spectral Deconvolution and Identification System NIST MS Search Tagfinder 63
AMDIS Raw data visualization 64
AMDIS Result visualization 65
NIST MS Search GUI 66
Software tools for Statistical Analysis 67
Stats and Machine Learning Commercial SIMCA Mass Profiler Professional (MPP) Agilent and more Free MetaboAnalyst R 68
MetaboAnalyst 69
Other software tools COMSPARI COMparison of SPectral And Retention Information MathDAMP Mathematica package for Differential Analysis of Metabolite Profiles MSFACTs and many more Metabolomics Spectral Formatting, Alignment and Conversion Tools 70
Thank You