MeltDBWiki/RoundingMZ - Revision history

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2011-10-26T06:13:07Z

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← Older revision	Revision as of 08:13, 26 October 2011
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imported>HeikoNeuweger at 20:12, 10 April 2008

2008-04-10T20:12:16Z

← Older revision		Revision as of 22:12, 10 April 2008
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	* Several mass spectral databases used for the identification of metabolites in GC/MS measurements (EI) contain mass spectra in nominal m/z notation whereas MS instruments are able to obtain higher resolution.		* Several mass spectral databases used for the identification of metabolites in GC/MS measurements (EI) contain mass spectra in nominal m/z notation whereas MS instruments are able to obtain higher resolution.
	* The mass spectral lookup using e.g. the ''dot-product' of the query and database spectra is ~~inaprropriate~~ if high resolution spectra are compared to spectra with nominal m/z entries. One possibility is to transform the high resolution spectra to integral m/z values. Alternatively, adapted scoring methods can be applied.		* The mass spectral lookup using e.g. the ''dot-product'' of the query and database spectra is inapropriate if high resolution spectra are compared to spectra with nominal m/z entries. One possibility is to transform the high resolution spectra to integral m/z values. Alternatively, adapted scoring methods can be applied.
	* High resolution mass spectra can be compared to nominal m/z spectra by ''rounding'' the measured m/z values to integral values.		* High resolution mass spectra can be compared to nominal m/z spectra by ''rounding'' the measured m/z values to integral values.
	* It is questionable if ''rounding'' at 0.5 is the best option.		* It is questionable if ''rounding'' at 0.5 is the best option.
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	[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]		[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]

	* For all ~~masses measured~~ by a MS instrument (EI, Ion Trap) ~~during~~ a complete chromatogram, the distribution of the values is comparable.		* For all m/z values detected by a MS instrument (EI, Ion Trap) for a complete chromatogram, the distribution of the values is comparable to that of the KEGG compounds.
	* Again, in the fractional interval 0.7 to 0.75 only 0.3% of the m/z values are detected.		* Again, in the fractional interval 0.7 to 0.75 only 0.3% of the m/z values are detected.

imported>HeikoNeuweger at 20:10, 10 April 2008

2008-04-10T20:10:20Z

imported>HeikoNeuweger at 19:56, 10 April 2008

2008-04-10T19:56:21Z

← Older revision		Revision as of 21:56, 10 April 2008
Line 25:		Line 25:

	[[Image:MeltDBWiki$$RoundingMZ$mzfrac.png]]		[[Image:MeltDBWiki$$RoundingMZ$mzfrac.png]]

			* This observation is also useful if extracted ion chromatograms (EIC) of GC/MS measurements with integral m/z values need to be generated without following individual m/z traces. Again, a ''rounding'' of the m/z values at the 0.7 instead of 0.5 will provide more stable EICs.

	[[Image:MeltDBWiki$$RoundingMZ$cdfhist.png]]		[[Image:MeltDBWiki$$RoundingMZ$cdfhist.png]]

imported>HeikoNeuweger at 19:48, 10 April 2008

2008-04-10T19:48:48Z

← Older revision		Revision as of 21:48, 10 April 2008
Line 17:		Line 17:
	* Mass spectrometric devices may drift, meassured m/z values can therefore vary.		* Mass spectrometric devices may drift, meassured m/z values can therefore vary.
	* To round m/z to integral values as robust as possible, 0.75 instead of 0.5 may be used.		* To round m/z to integral values as robust as possible, 0.75 instead of 0.5 may be used.
	* In the fractional interval 0.~~725~~ to 0.~~775~~ only 15 compounds are listed in the KEGG compounds database.		* In the fractional interval 0.7 to 0.75 only 15 compounds are listed in the KEGG compounds database.

	[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]		[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]

	* For all masses measured by a MS instrument (Ion Trap) during a complete chromatogram, the distribution of the values is comparable.		* For all masses measured by a MS instrument (Ion Trap) during a complete chromatogram, the distribution of the values is comparable.
	* ~~Here~~, in the fractional interval 0.6 to 0.65 only ~~15 compounds~~ are ~~listed in the KEGG compounds database~~.		* Again, in the fractional interval 0.7 to 0.75 only 0.3% of the m/z values are detected.

	[[Image:MeltDBWiki$$RoundingMZ$mzfrac.png]]		[[Image:MeltDBWiki$$RoundingMZ$mzfrac.png]]

	[[Image:MeltDBWiki$$RoundingMZ$cdfhist.png]]		[[Image:MeltDBWiki$$RoundingMZ$cdfhist.png]]

imported>HeikoNeuweger at 19:41, 10 April 2008

2008-04-10T19:41:27Z

← Older revision		Revision as of 21:41, 10 April 2008
Line 20:		Line 20:

	[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]		[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]

			* For all masses measured by a MS instrument (Ion Trap) during a complete chromatogram, the distribution of the values is comparable.
			* Here, in the fractional interval 0.6 to 0.65 only 15 compounds are listed in the KEGG compounds database.

			[[Image:MeltDBWiki$$RoundingMZ$mzfrac.png]]

			[[Image:MeltDBWiki$$RoundingMZ$cdfhist.png]]

imported>HeikoNeuweger at 17:54, 10 April 2008

2008-04-10T17:54:36Z

← Older revision		Revision as of 19:54, 10 April 2008
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	<!-- ##language:en -->		<!-- ##language:en -->

	== Round m/z values of mass spectra to ~~nominal~~ values ==		== Round m/z values of mass spectra to integral values ==

	* Several ~~Mass Spectral~~ databases contain mass spectra in nominal m/z notation.		* Several mass spectral databases contain mass spectra in nominal m/z notation whereas MS instruments are able to obtain higher resolution.
	* KEGG compounds database contains more than 10000 compounds with annotated masses		* High resolution mass spectra can be compared to nominal m/z spectra by rounding the measured m/z values to integral values.
	* Most of the masses are ~~around~~ 1000 Dalton.		* The KEGG compounds database contains more than 10000 compounds with annotated masses and most of the masses are below 1000 Dalton.
			* C, H, N, O, P, S are the main atoms of biological compounds.

	[[Image:MeltDBWiki$$RoundingMZ$histweight.png]]		[[Image:MeltDBWiki$$RoundingMZ$histweight.png]]

	* The possible ~~decimal~~ values of the ~~compounds~~ are dependent on the ~~actual compounds~~ mass.		* The possible fractional values of the compound masses are dependent on the integral compound mass.

	[[Image:MeltDBWiki$$RoundingMZ$scatter.png]]		[[Image:MeltDBWiki$$RoundingMZ$scatter.png]]

	* To round m/z to ~~integer~~ values as ~~robust~~ robust as possible, 0.75 instead of 0.5 ~~can~~ be used.		* Mass spectrometric devices may drift, meassured m/z values can therefore vary.
			* To round m/z to integral values as robust as possible, 0.75 instead of 0.5 may be used.
			* In the fractional interval 0.725 to 0.775 only 15 compounds are listed in the KEGG compounds database.

	[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]		[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]

imported>HeikoNeuweger at 17:42, 10 April 2008

2008-04-10T17:42:41Z

← Older revision		Revision as of 19:42, 10 April 2008
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	* To round m/z to integer values as robust robust as possible, 0.75 instead of 0.5 can be used.		* To round m/z to integer values as robust robust as possible, 0.75 instead of 0.5 can be used.

	[[Image:MeltDBWiki$$RoundingMZ$~~hist~~.png]]		[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]

imported>HeikoNeuweger at 17:26, 10 April 2008

2008-04-10T17:26:12Z

New page

__NOTOC__


== Round m/z values of mass spectra to nominal values ==

* Several Mass Spectral databases contain mass spectra in nominal m/z notation.
* KEGG compounds database contains more than 10000 compounds with annotated masses
* Most of the masses are around 1000 Dalton.

[[Image:MeltDBWiki$$RoundingMZ$histweight.png]]

* The possible decimal values of the compounds are dependent on the actual compounds mass.

[[Image:MeltDBWiki$$RoundingMZ$scatter.png]]

* To round m/z to integer values as robust robust as possible, 0.75 instead of 0.5 can be used.

[[Image:MeltDBWiki$$RoundingMZ$hist.png]]

← Older revision		Revision as of 22:10, 10 April 2008
Line 4:		Line 4:
	== Round m/z values of mass spectra to integral values ==		== Round m/z values of mass spectra to integral values ==

	* Several mass spectral databases contain mass spectra in nominal m/z notation whereas MS instruments are able to obtain higher resolution.		* Several mass spectral databases used for the identification of metabolites in GC/MS measurements (EI) contain mass spectra in nominal m/z notation whereas MS instruments are able to obtain higher resolution.
	* High resolution mass spectra can be compared to nominal m/z spectra by rounding the measured m/z values to integral values.		* The mass spectral lookup using e.g. the ''dot-product' of the query and database spectra is inaprropriate if high resolution spectra are compared to spectra with nominal m/z entries. One possibility is to transform the high resolution spectra to integral m/z values. Alternatively, adapted scoring methods can be applied.
			* High resolution mass spectra can be compared to nominal m/z spectra by ''rounding'' the measured m/z values to integral values.
			* It is questionable if ''rounding'' at 0.5 is the best option.
	* The KEGG compounds database contains more than 10000 compounds with annotated masses and most of the masses are below 1000 Dalton.		* The KEGG compounds database contains more than 10000 compounds with annotated masses and most of the masses are below 1000 Dalton.
	* C, H, N, O, P, S are the main atoms of ~~biological~~ compounds.		* C, H, N, O, P, S are the main atoms of biologically relevant compounds.

	[[Image:MeltDBWiki$$RoundingMZ$histweight.png]]		[[Image:MeltDBWiki$$RoundingMZ$histweight.png]]
Line 15:		Line 17:
	[[Image:MeltDBWiki$$RoundingMZ$scatter.png]]		[[Image:MeltDBWiki$$RoundingMZ$scatter.png]]

			* In the fractional interval 0.7 to 0.75 only 15 compounds are listed in the KEGG compounds database.
	* Mass spectrometric devices may drift, meassured m/z values can therefore vary.		* Mass spectrometric devices may drift, meassured m/z values can therefore vary.
	* To round m/z to integral values as robust as possible, 0.75 instead of 0.5 may be used.		* To round m/z to integral values as robust as possible, 0.7 instead of 0.5 may be used.
	* In the fractional interval 0.7 to 0.75 only 15 compounds are listed in the KEGG compounds database.

	[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]		[[Image:MeltDBWiki$$RoundingMZ$histmz.png]]

	* For all masses measured by a MS instrument (Ion Trap) during a complete chromatogram, the distribution of the values is comparable.		* For all masses measured by a MS instrument (EI, Ion Trap) during a complete chromatogram, the distribution of the values is comparable.
	* Again, in the fractional interval 0.7 to 0.75 only 0.3% of the m/z values are detected.		* Again, in the fractional interval 0.7 to 0.75 only 0.3% of the m/z values are detected.

	[[Image:MeltDBWiki$$RoundingMZ$mzfrac.png]]		[[Image:MeltDBWiki$$RoundingMZ$mzfrac.png]]

	* This observation is also useful if extracted ion chromatograms (EIC) of GC/MS measurements with integral m/z values need to be generated without following individual m/z traces. Again, a ''rounding'' of the m/z values at ~~the~~ 0.7 instead of 0.5 will provide more stable EICs.		* This observation is also useful if extracted ion chromatograms (EIC) of GC/MS measurements with integral m/z values need to be generated without following individual m/z traces. Again, a ''rounding'' of the m/z values at 0.7 instead of 0.5 will provide more stable EICs.

	[[Image:MeltDBWiki$$RoundingMZ$cdfhist.png]]		[[Image:MeltDBWiki$$RoundingMZ$cdfhist.png]]