intro to data preprocessing€¦ · Data preprocessing workflow 20 GC-MS LC-MS detect masses from...
Transcript of intro to data preprocessing€¦ · Data preprocessing workflow 20 GC-MS LC-MS detect masses from...
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Xiuxia Du, Ph.D. Department of Bioinformatics and Genomics
University of North Carolina at Charlotte
Introduction to Preprocessing of Untargeted Metabolomics Data
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Outline• Raw untargeted LC/MS and GC/MS metabolomics data
- Profile and centroid data
- Mass vs. retention time map
- TIC
- EIC
• Principles of LC/MS and GC/MS data preprocessing
• Feature identification
- Identification of known compounds
- Identification of unknown compounds
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Raw Untargeted LC/MS and GC/MS Metabolomics data
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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
List of mass spectra
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One mass spectrum
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One mass spectrum
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One mass spectrum
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Zoom in one mass spectrum
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profile mode
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Mass spectra in centroid mode
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Mass spectra in centroid mode
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Spectrum in centroid mode• Data files are much smaller than files in profile mode.
• We will use the centroid data for practicing data pre-processing using XCMS and MZmine 2.
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LC-MS raw data in 3D
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Raw data in 3D
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3D to 2D• Direct processing of the 3D data is NOT trivial
• Instead, we examine 2D
- Mass vs. retention time
- Total ion current vs. retention time: TIC
- Ion current vs. retention time for a particular mass: EIC (Extracted Ion Chromatogram)
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Mass vs. retention time map
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TIC
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EIC
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EIC
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Principles of LC/MS and GC/MS Data Preprocessing
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Data preprocessing workflow
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GC-MS
LC-MSdetect masses from
mass spectra
detect masses frommass spectra
constructEICs
constructEICs
detectchromatographic peaks
detectchromatographic peaks
deconvolution
annotation
databasesearch
databasesearch
1 2 3 4 5 6alignment /
correspondence
alignment / correspondence
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Construct EICs
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Select one EIC
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One EIC
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Detect EIC peaks
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• Use wavelet transform
• Implemented in XCMS as the centWave method
Detect EIC peaks
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mexican hat wavelet
−20 −10 0 10 20
−0.4
0.0
0.2
0.4
0.6
0.8
t
ψψs,ττ((
t))
s = 1s = 2s = 8
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1012
1:dim(wCoefs)[1]
Scal
e
+
++
2850 2900 2950 3000 3050 3100 3150
02
46
810
Seconds
Inte
nsity
* 10
3
ChromatogramGaussian Fit
Tautenhahn, R.; Bottcher, C.; Neumann, S., Highly sensitive feature detection for high resolution LC/MS. BMC bioinformatics 2008, 9, 504.
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Detected EIC peaks
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LC/MS-specific Data Preprocessing
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Find isotopes
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Find isotopes
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Find isotopes
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Alignment
zoom in……
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Alignment
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Alignment
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Peaks table after alignment
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GC/MS-specific Data Preprocessing
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GC-EI-MS
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• Example: EI fragmentation of methanol
EI fragmentation
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[CH3OH]•+ �! CH3O+ +H•
[CH3OH]•+ �! CH2O+ +H2
[CH3OH]•+ �! CH+3 + •OH
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Deconvolution
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ADAP-GC 2.0
ADAP-GC 2.0: Deconvolution of Coeluting Metabolites from GC/TOF-MS Data for Metabolomics Studies. Analytical chemistry 2012, 84 (15), 6619-29.
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Feature identification
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Feature identification• Apply statistics and machine learning to detect
discriminating peaks
• Identify discriminating peaks
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Identification of known compounds• Screening search for compound ID based on LC-MS
data
- Searching monoisotopic mass and isotopic distribution against compound databases
• Library match for compound identification from both LC-MS/MS and GC-MS spectra
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HMDB
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HMDB
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MS/MS or GC-MS spectra matching• Library match for compound identification from both
LC-MS/MS and GC-MS spectra
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Identification of unknown compounds• MS-FINDER
• CSI:FingerID
• CFM-ID
• MetFrag
• MIDAS
• MAGMA
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MetFrag
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More on identification
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More on identification
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More on identification
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More on identification• Information we have for identification of compounds
based on MS/MS
- M+H
- Experimental isotopic identification
- MS/MS
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• Compare isotopic distributions
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theoretical experimental
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• CompareMS/MS
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library
experimental
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Thank you!