MeltDBWiki/Profiling - Revision history

Admin: 7 revisions

2011-10-26T06:17:24Z

7 revisions

← Older revision	Revision as of 08:17, 26 October 2011
(No difference)

imported>HeikoNeuweger at 08:56, 8 April 2009

2009-04-08T08:56:06Z

← Older revision		Revision as of 10:56, 8 April 2009
Line 25:		Line 25:

	- 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

			[[Image:MeltDBWiki$$Profiling$fbca.png]]

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

imported>HeikoNeuweger at 08:54, 8 April 2009

2009-04-08T08:54:31Z

imported>HeikoNeuweger at 08:52, 8 April 2009

2009-04-08T08:52:19Z

← Older revision		Revision as of 10:52, 8 April 2009
Line 30:		Line 30:
	- 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

			---- /!\ '''Edit conflict - other version:''' ----
	[[Image:MeltDBWiki$$Profiling$profiling.png]]		[[Image:MeltDBWiki$$Profiling$profiling.png]]

			---- /!\ '''Edit conflict - your version:''' ----
			[[Image:MeltDBWiki$$Profiling$profiling.png]]

			---- /!\ '''End of edit conflict''' ----

	- 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.		- 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.

imported>HeikoNeuweger at 08:50, 8 April 2009

2009-04-08T08:50:39Z

← Older revision		Revision as of 10:50, 8 April 2009
Line 30:		Line 30:
	- 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

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

imported>HeikoNeuweger at 08:44, 8 April 2009

2009-04-08T08:44:10Z

← Older revision		Revision as of 10:44, 8 April 2009
Line 7:		Line 7:

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

			[[Image:MeltDBWiki$$Profiling$ra.png]]

			- Select one of the XCMS based peak detection tools and start the analysis

	[[Image:MeltDBWiki$$Profiling$xcms.png]]		[[Image:MeltDBWiki$$Profiling$xcms.png]]

imported>HeikoNeuweger at 08:25, 8 April 2009

2009-04-08T08:25:06Z

← Older revision		Revision as of 10:25, 8 April 2009
Line 4:		Line 4:
	- 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
Line 24:		Line 26:
	- 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)
Line 33:		Line 34:
	- 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]]

imported>HeikoNeuweger at 19:30, 7 April 2009

2009-04-07T19:30:22Z

New page

__NOTOC__
== Profiling in MeltDB ==

- 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

attachement:xcms.png

- 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.

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

attachement:tic.png

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

attachement: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

attachement: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 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)

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

attachement:alignment.png

← Older revision		Revision as of 10:54, 8 April 2009
Line 2:		Line 2:
	== Profiling in MeltDB ==		== Profiling in MeltDB ==

	- 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

	- Open your experiment		- Open your experiment

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

	[[Image:MeltDBWiki$$Profiling$ra.png]]		[[Image:MeltDBWiki$$Profiling$ra.png]]

	- Select one of the XCMS based peak detection tools and start the analysis		- Select one of the XCMS based peak detection tools and start the analysis

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

	[[Image:MeltDBWiki$$Profiling$tic.png]]		[[Image:MeltDBWiki$$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.

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

	- Depending on the number of chromatograms in your experiment this may take a while		- 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		- Navigate back to your experiment and run the 'MeltDB Profiling' tool via the 'Run analysis' action

	~~---- /!\ '''Edit conflict - other version:''' ----~~
	[[Image:MeltDBWiki$$Profiling$profiling.png]]		[[Image:MeltDBWiki$$Profiling$profiling.png]]

	~~---- /!\ '''Edit conflict - your version:''' ----~~		- The MeltDB profiling tool iterates through all peaks in the selected reference chromatogram. Matching peaks in the aligned chromatograms are detected 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.
	~~[[Image:MeltDBWiki$$Profiling$profiling.png]]~~

	~~---- /!\ '''End of edit conflict''' ----~~

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

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