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1/15/2014
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Other software for metabolomics data analysis
Stephen Barnes, PhD
Paul H. Benton, PhD
Xiuxia Du, PhD
Software
• MarkerView™ ‐ AB Sciex• Progenesis CoMet – Nonlinear DynamicsProgenesis CoMet Nonlinear Dynamics• TransOmics – Waters• Mass Hunter – Agilent• Molfind – downloadable – free• metAlign• MZmineXCMS 2• XCMS 2
• metaXCMS• MAVEN
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MarkerView™ Software (AB Sciex)• Designed for metabolomics and
protein/peptide biomarker profiling applications
– Allows rapid and easy data review to determine up‐ and down‐regulation of endogenous compounds in complex samples.
– Mass and retention time alignment
– Classified and non‐classified workflows ‐ PCA, T‐tests, etc.workflows PCA, T tests, etc.
– Powerful PCVG analysis for immediate recognition of groups and biological trends
• Supports the AB SCIEX TripleTOF™ 5600 System, QTRAP® Systems, and TOF/TOF Systems
MarkerView™ Software (AB Sciex)
− PCVG analysis color‐codes groups of identifications h d lthat demonstrate similar behaviors
− Easily pick out trends by profiling the response across the samples
− Links PCA analysis back to protein or peptide identification results
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Import DataImport Data
Retention time
alignment
Retention time
alignment
Co‐detect, Quantify
and Normalise
Co‐detect, Quantify
and Normalise
Collate ion forms Collate
ion forms
Identify, Review + Report
Identify, Review + Report
Progenesis CoMet workflow schematic
NormaliseNormalise
RT
m/z
Identification• MetaScope, our search tool, is integrated into the software
– Search your own data and return compound identifications, including chemical structures from SDF databases
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metAlign (I)
• Features:Format conversion– Format conversion
– accurate mass calculations
– baseline corrections
– peak picking
– saturation and mass peak artifact filtering
– alignmentalignment
• Availability– Free
– www.metalign.nl
metAlign (II)
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metAlign (III)
MZmine (I)
workflow
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MZmine (II)visualization
MZmine (III)
peakdetection (I)
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MZmine (IV)
peakdetection (II)
peak identification
MZmine (V)
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MZmine (VI)
• Availability
– Free
– http://mzmine.sourceforge.net/index.shtml
XCMS 2
• Availability
– Open source
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metaXCMS (I)
metaXCMS (II)
• Availability
– Free
– http://metlin.scripps.edu/metaxcms/index.php
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MAVEN (I)
• Featureschromatographic alignment– chromatographic alignment
– peak feature detection
– isotope and adduct calculator
– formula predictor
– pathway visualization
• AvailabilityAvailability– Free
– http://genomics‐pubs.princeton.edu/mzroll/index.php?show=index
MAVEN (II)
multi‐file EIC viewEIC view
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MAVEN (III)
pathway viewview
MAVEN (IV)
compound identificationidentification
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MAVEN (V)
peak detectiondetection
Other useful links
• Metabonews– http://www.metabonews.ca/archive.html
– You can subscribe to get monthly newsletter
• Metabolomics Society– http://www.metabolomicssociety.org/
• Regional Comprehensive Metabolomics Research Centers– RTI Intl – [email protected]
– UC‐Davis – ofienh@ucdavis eduUC Davis [email protected]
– U. Michigan – [email protected]
– U. Florida – [email protected]
– Mayo – [email protected]
– U Kentucky – [email protected]
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