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Smart Templates for Chemical Identification in GCxGC-MS. QingPing Tao 1 , Stephen E. Reichenbach 2 , Mingtian Ni 3 , Arvind Visvanathan 2 , Michael Kok 2 , Luke L. Waltman 1 1 GC Image, LLC, Lincoln, NE 2 Computer Science & Engineering Dept., University of Nebraska-Lincoln

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smart templates for chemical identification in gcxgc ms

Smart Templates for Chemical Identification in GCxGC-MS

QingPing Tao1, Stephen E. Reichenbach2,

Mingtian Ni3, Arvind Visvanathan2, Michael Kok2, Luke L. Waltman1

1GC Image, LLC, Lincoln, NE

2Computer Science & Engineering Dept., University of Nebraska-Lincoln

3Microsoft Corp., Redmond, WA

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide2
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

GCxGCPeak Template MatchingSmart TemplatesBuilding Smart Multi-type TemplatesConclusions and Future Work

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide3
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

GCxGC

Objective of GCxGC Analysis

Chemical Identification

Outline

GCxGC

  • Two independent separations for the entire sample
  • GCxGC data can be processed as a digital image
  • Mass spectrometry (MS) data provides rich information for identification

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide4
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

GCxGC

Objective of GCxGC Analysis

Chemical Identification

Outline

GCxGC

GC Chromatogram

GCxGC Total Ion Chromatogram

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide5
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

GCxGC

Objective of GCxGC Analysis

Chemical Identification

Outline

Objective of GCxGC Analysis

  • Separate individual peaks from background
  • Quantify each peak
  • Identify the peaks for chemicals of interest

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide6
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

GCxGC

Objective of GCxGC Analysis

Chemical Identification

Outline

Chemical Identification with GCxGC

  • Automated approaches
    • Library search
      • Such as NIST Mass Spectral Library
    • Rule-based techniques:
      • Such as constrain expressions based on retention times or mass spectrum
    • Pattern matching: markers, chemical retention pattern.
  • Challenges:
    • Data inconsistencies: retention time variations
    • Data and task complexities: multi-dimension, many peaks
  • Solution: combined approach (“Smart templates”) with peak template matching constraint expressions

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide7
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

GCxGC

Objective of GCxGC Analysis

Chemical Identification

Outline

Outline

  • Peak template matching
  • Smart Templates
    • Computer Language for Identifying Chemicals (CLIC)
    • Smart Template
      • Peak template matching with CLIC
  • Building Smart Multi-type Templates
    • Interactive tools for building smart multi-type templates
    • Automatically generating CLIC for peaks
    • Automatically generating peak sets with markers.
  • Conclusion and Future Works

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide8
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Chemical Identification Process

Fundamental Difficulty

Peak Template Matching

  • Identify compounds by matching previously known peaks to unidentified peaks
  • A peak template is a set of annotated peaks with:
    • Computed features such as peak location (2D retention times)
    • Assigned information such as compound name
  • A target peak is a set of unannotated peaks that have computed features
  • Peak template matching tries to establish as many correspondences as possible from template peaks to target peaks

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide9
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Chemical Identification Process

Fundamental Difficulty

Chemical Identification Process

  • Construct a peak template:
    • Created by a chemist through interactive annotation
  • Match template and target peaks
  • Apply the template: assign information from template to target peaks

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide10
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Chemical Identification Process

Fundamental Difficulty

Fundamental Difficulty of Peak Template Matching

  • Peak pattern distortions:
    • Peaks for the same compound may appear at different retention times in different images
  • Basic solution:
    • Search all allowable matches from template peaks to target peaks under some retention time windows
    • Find a transformation that maximize the number of matched peaks

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide11
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Chemical Identification Process

Fundamental Difficulty

B2

peak1

B1

B3

Fundamental Difficulty of Peak Template Matching

  • Challenges:
    • Searching transformations in a large space is computationally expensive
    • False identifications may happen when two target peaks are very close together
  • A solution: Smart Template

peak2

B2

peak1

B1

B3

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide12
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Computer Language for Identifying Chemicals (CLIC)

Example CLIC Expressions

Peak Template Matching with CLIC

Smart Templates

  • Objective:
    • Reduce the number of allowable matchings
    • Reduce ambiguous matchings
    • Reduce human intervention
  • Approach:
    • Add more constraints other than retention time patterns
    • CLIC

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide13
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Computer Language for Identifying Chemicals (CLIC)

Example CLIC Expressions

Peak Template Matching with CLIC

Computer Language for Identifying Chemicals (CLIC)

CLIC [Reichenbach et al., 2004] is a language to express constraints on GCxGC retention times, peak characteristics, and mass spectral characteristics:

  • Functions of retention times
  • Functions of peak characteristics
  • Functions of mass spectra
  • Logical and arithmetic operators
    • Comparative operators: <, ≤, >, ≥, =, ≠
    • Addition, subtraction, negation (-) and parentheses
    • Logical operators: and(&), or (|), and negation(!)

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide14
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Computer Language for Identifying Chemicals (CLIC)

Example CLIC Expressions

Peak Template Matching with CLIC

Computer Language for Identifying Chemicals (CLIC)

Functions characterizing chromatographic properties and mass spectral characteristics are key features of CLIC.

  • Retention(2) returns the retention time of the peak on the second column.
  • Intensity(40) returns the intensity value of the indicated channel (m/z = 40) in the mass spectrum of the peak.
  • Ordinal(40) returns the ordinal position of the indicated channel (m/z = 40 in a mass spectrum) in the intensity-ordered multi-channel array of the peak.

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide15
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Computer Language for Identifying Chemicals (CLIC)

Example CLIC Expressions

Peak Template Matching with CLIC

Example CLIC Expressions

  • Alkanes
  • Criteria (Welthagen et al. 2003): Base peak 57 or 71 and second largest peak 71 or 57. No time rule is needed for this group, but a retention window of 1.0 – 1.5s can be used.
  • CLIC Expression:
    • (Ordinal(57) ≤ 2) & (Ordinal(71) ≤ 2)& (Retention(2) ≥ 1.0) & (Retention(2) ≤ 1.5)

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide16
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Computer Language for Identifying Chemicals (CLIC)

Example CLIC Expressions

Peak Template Matching with CLIC

B2

peak1

B1

B3

Peak Template Matching with CLIC

  • Each peak in the template has an optional CLIC expression
    • First, find a set of possible matches by using the retention time pattern
    • Then, prune the matching space based on CLIC expressions
    • Finally, search for the best matching
    • The combination of chromatographic retention time patterns and CLIC expressions can improve both speed and accuracy of automated chemical identification for GCxGC
    • We call it a Smart template

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide17
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Building Smart Multi-type Templates

Smart Template has been implemented in GC Image® software.

  • Interactive tools for building Multi-type Templates
    • Peaks, groups, graphics, text objects and chemical structures
  • Interactive tools for building CLIC expressions
    • A GUI that resembles a calculator for users to create and test CLIC expressions
    • An interface for specifying a CLIC expression for each template peak
  • Interfaces to match and apply templates

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide18
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart template

Auto CLIC

Auto chemical grouping with markers

Build Multi-type template

Construct and edit template with peaks and other structures:

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide19
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Build Smart Template – Example with Grob Mix

1) Build a template from the original image

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide20
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Build Smart Template – Example with Grob Mix

2) Wrong match because of peak pattern distortions:

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide21
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Build Smart Template – Example with Grob Mix

3) Smart template solution:

a) Create CLIC expression for Nonanal

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide22
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Build Smart Template – Example with Grob Mix

b) Specify CLIC expression for Nonanal template peak:

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide23
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Build Smart Template – Example with Grob Mix

4) Matching with Smart Template:

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide24
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Auto CLIC

Automatically generate CLIC expressions for peaks:

  • CLIC function: Match()
    • NIST matching function returns the similarity between two mass spectra
      • Value range is [0, 1000]
      • Higher is the value, more similar are the two mass spectra
  • CLIC expression, Match(“”) > threshold, can be used to identify chemicals.
    • The mass spectrum of the peak is
    • Automatically generate the threshold

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide25
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Auto CLIC

Automatically generate matching threshold:

  • The similarities between this peak and all other peaks should be less than the threshold
  • The threshold has the large margins from this peak and all other peaks
  • For example: peak 1 represents blob B1
    • B1. Match(“”) = 1000
    • B2. Match(“”) = 600
    • B3. Match(“”) = 400
    • Match(“”) > 800

B1

peak1

800

B2

B3

B2

B1

B3

600

1000

400

0

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide26
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Auto CLIC

1) Set Auto CLIC function

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide27
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart Template

Auto CLIC

Auto chemical grouping with markers

Auto CLIC

2) Generate CLIC

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide28
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart template

Auto CLIC

Auto chemical grouping with markers

Auto chemical grouping with markers

Group peaks based on their retention time patterns:

  • Build natural clusters of peaks
  • Each cluster is represented by a polygon
  • A template may consist of a set of groups (polygons)

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide29
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart template

Auto CLIC

Auto chemical grouping with markers

Auto chemical grouping with markers

29 clusters created by single linkage hierarchical clustering algorithm

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide30
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart template

Auto CLIC

Auto chemical grouping with markers

Auto chemical grouping with markers

Automatically generate markers for groups (polygons)

  • Template matching is based on peaks
  • Each group needs markers
    • A marker is a significant peak in the group
    • Markers are at evenly distributed locations to represent the retention time pattern of the group
  • Auto marker:
    • Cluster all peaks in a group
    • Pick the largest peak in each cluster as a marker

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide31
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart template

Auto CLIC

Auto chemical grouping with markers

Auto chemical grouping with markers

1) Set Auto Marker function

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide32
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart template

Auto CLIC

Auto chemical grouping with markers

Auto chemical grouping with markers

2) Generate markers

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide33
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Build Multi-type template

Build Smart template

Auto CLIC

Auto chemical grouping with markers

Auto chemical grouping with markers

2) Generate markers

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide34
Introduction

Peak Template Matching

Smart Templates

Building Smart Multi-type Templates

Conclusions and Future Work

Conclusions and Future Work

  • Smart Template matching can be used to automatically identify chemicals in GCxGC-MS data
  • The combination of retention time patterns and constraints greatly reduces ambiguity and speeds processing
  • Future work:
    • Enhanced GUI
    • More CLIC functions
    • Semi-automated or automated template construction
      • Auto CLIC and Auto Marker are just two first steps

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

slide35
Introduction

Peak Template Matching

Computer Language for Identifying Chemicals Peak Template Matching with CLIC

Conclusions and Future Work

Current work is supported by NSF and NIH

Questions?

Software: [email protected]

www.gcimage.com

Licensing: [email protected]

www.zoex.com

Q. Tao, S. E. Reichenbach, et al.

Multi-type Templates in GCxGC-MS

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