MeltDBWiki/Profiling: Difference between revisions

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  - You have already uploaded your chromatograms and organized them into Chromatogram Groups and an Experiment
  - You have already uploaded your chromatograms and organized them into Chromatogram Groups and an Experiment


  - Next step is to perform a XCMS based peak detection. Select 'Run analysis' im the experiment context
  - Open your experiment


attachement:xcms.png
- Next step is to perform a XCMS based peak detection. Select 'Run analysis' in the experiment context


  - After the XCMS peak detection jab has been submitted to the compute cluster and finished, review the results using the 'Show TIC' action of your experiment.
  [[Image:MeltDBWiki$$Profiling$xcms.png]]


  - Select one chromatogram that features at least 30 peaks and does not contain artefacts and to much ''saturated'' peaks
  - After the XCMS peak detection job has been submitted to the compute cluster and finished, review the results using the 'Show TIC' action of your experiment.


attachement:tic.png
- Select one chromatogram that features at least 30 peaks and does not contain artifacts and to much ''saturated'' peaks
 
[[Image:MeltDBWiki$$Profiling$tic.png]]


  - For this chromatogram, compute the FBCA based alignments using the 'Compute alignment' action.
  - For this chromatogram, compute the FBCA based alignments using the 'Compute alignment' action.


attachement:alignment.png
[[Image:MeltDBWiki$$Profiling$alignment.png]]


  - Select FBCA, your current experiment and the XCMS peak detection tool you just applied
  - Select FBCA, your current experiment and the XCMS peak detection tool you just applied
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  - Navigate back to your experiment and run the 'MeltDB Profiling' tool via the 'Run analysis' action
  - Navigate back to your experiment and run the 'MeltDB Profiling' tool via the 'Run analysis' action


attachement:alignment.png
[[Image:MeltDBWiki$$Profiling$alignment.png]]


  - The MeltDB profiling tool iterates through all peaks in the selected reference chromatogram for the FBCA alignment  
  - The MeltDB profiling tool iterates through all peaks in the selected reference chromatogram for the FBCA alignment and find matching peaks in the aligned chromatograms using mass spectral similarity (cosine score) and chromatographic proximity. If a common EIC peak can be detected in more than 80 % of the chromatograms, a mass spectral tag is annotated using the median retention time and the m/z value of the most abundant common EIC.
and find matching peaks in the aligned chromatograms using mass spectral similarity (cosine score) and chromatographic proximity. If a common EIC peak can be detceted in more than 80 % of the chromatograms, a mass spectral tag is annotated using the median retention time and the m/z value of the common EIC.


  - Review the detected Mass Spectral tags in the TIC view of your experiment (green peak markers)
  - Review the detected Mass Spectral tags in the TIC view of your experiment (green peak markers)
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  - You are now able to perform statistical and exploratory analysis (Boxplot, ICA, PCA, etc) on the detected Tags.
  - You are now able to perform statistical and exploratory analysis (Boxplot, ICA, PCA, etc) on the detected Tags.


attachement:alignment.png
[[Image:MeltDBWiki$$Profiling$pca-profiling.png]]

Revision as of 09:25, 8 April 2009

Profiling in MeltDB

- You have already uploaded your chromatograms and organized them into Chromatogram Groups and an Experiment

- Open your experiment

- Next step is to perform a XCMS based peak detection. Select 'Run analysis' in the experiment context

MeltDBWiki$$Profiling$xcms.png

- After the XCMS peak detection job has been submitted to the compute cluster and finished, review the results using the 'Show TIC' action of your experiment.

- Select one chromatogram that features at least 30 peaks and does not contain artifacts and to much saturated peaks

MeltDBWiki$$Profiling$tic.png

- For this chromatogram, compute the FBCA based alignments using the 'Compute alignment' action.

MeltDBWiki$$Profiling$alignment.png

- Select FBCA, your current experiment and the XCMS peak detection tool you just applied

- Depending on the number of chromatograms in your experiment this may take a while

- Navigate back to your experiment and run the 'MeltDB Profiling' tool via the 'Run analysis' action

MeltDBWiki$$Profiling$alignment.png

- The MeltDB profiling tool iterates through all peaks in the selected reference chromatogram for the FBCA alignment and find matching peaks in the aligned chromatograms using mass spectral similarity (cosine score) and chromatographic proximity. If a common EIC peak can be detected in more than 80 % of the chromatograms, a mass spectral tag is annotated using the median retention time and the m/z value of the most abundant common EIC.

- Review the detected Mass Spectral tags in the TIC view of your experiment (green peak markers)

- You are now able to perform statistical and exploratory analysis (Boxplot, ICA, PCA, etc) on the detected Tags.

MeltDBWiki$$Profiling$pca-profiling.png
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