Peak Detection - Revision history

Laschp: /* Peak picking - basic concepts */

2026-03-08T05:57:43Z

Peak picking - basic concepts

← Older revision		Revision as of 07:57, 8 March 2026
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	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>x</math>		\|<math>x</math>
	\|the x-vector (in Th units) ranging from mzlow to mzhigh (~~2000~~ - 13000 Th per default)		\|the x-vector (in Th units) ranging from mzlow to mzhigh (3000 - 13000 Th per default)
	\|}		\|}

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:19:45Z

Peak picking - basic concepts

← Older revision		Revision as of 16:19, 8 October 2025
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	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>x_{c}</math>		\|<math>x_{c}</math>
	\|'center' of the sigmoidal function, denotes the x-position at which asymptote maximum (pos, or neg) ~~growth~~ occurs		\|'center' of the sigmoidal function, denotes the x-position at which asymptote maximum growth (pos, or neg) occurs
	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>x</math>		\|<math>x</math>

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:18:12Z

Peak picking - basic concepts

← Older revision		Revision as of 16:18, 8 October 2025
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	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>I_{m}</math>		\|<math>I_{m}</math>
	\|mean of the 13(-3) most intense mass peaks in the m/z range [mzlow mzhigh] of the given spectrum - 13(-3) means that the top 3 ~~peak~~ are ignored		\|mean of the 13(-3) most intense mass peaks in the m/z range [mzlow mzhigh] of the given mass spectrum, 13(-3) means that the top 3 mass peaks are ignored
	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>s</math>		\|<math>s</math>

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:17:13Z

Peak picking - basic concepts

← Older revision		Revision as of 16:17, 8 October 2025
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	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>T_{m/z}</math>		\|<math>T_{m/z}</math>
	\|the intensity threshold function, i.e. the S-shaped sigmoid function ~~according to (ii)~~		\|the intensity threshold function, i.e. the S-shaped sigmoid function
	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>I_{m}</math>		\|<math>I_{m}</math>

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:16:28Z

Peak picking - basic concepts

← Older revision		Revision as of 16:16, 8 October 2025
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	:i) A baseline function obtained by [https://wiki-ms.microbe-ms.com/index.php?title=Spectral_Pre-processing#Baseline_subtraction baseline correction by asymmetric least squares],		:i) A baseline function obtained by [https://wiki-ms.microbe-ms.com/index.php?title=Spectral_Pre-processing#Baseline_subtraction baseline correction by asymmetric least squares],

	:ii) a S-shaped sigmoid function that reflects MALDI-ToF MS sensitivity as a function of m/z values, and		:ii) a S-shaped sigmoid function <math>T_{m/z}</math> that reflects MALDI-ToF MS sensitivity as a function of m/z values, and

	:iii) the noise distribution function multiplied by a constant.		:iii) the noise distribution function multiplied by a constant.

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:15:26Z

Peak picking - basic concepts

← Older revision		Revision as of 16:15, 8 October 2025
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	:iii) the noise distribution function multiplied by a constant.		:iii) the noise distribution function multiplied by a constant.

	[[File:Threshold-for-peak-picking.jpg\|600px\|thumb\|right\| Sigmoidal function ~~(ii)~~ <math>T_{m/z}</math> used for peak picking. Note that the parameters indicated are used for illustration purposes and are generally not recommended for peak picking. The slope parameter ''l'' which equals 5.5 in this example (default is 7.5) defines the the slope of the curve at the x-position <math>x_{c}</math>. The latter parameter defines the point at which asymptote maximum (pos, or neg) growth occurs (in this example at <math>x_{c}</math> = 8000 Th).]]		[[File:Threshold-for-peak-picking.jpg\|600px\|thumb\|right\| Sigmoidal function <math>T_{m/z}</math> used for peak picking. Note that the parameters indicated are used for illustration purposes and are generally not recommended for peak picking. The slope parameter ''l'' which equals 5.5 in this example (default is 7.5) defines the the slope of the curve at the x-position <math>x_{c}</math>. The latter parameter defines the point at which asymptote maximum (pos, or neg) growth occurs (in this example at <math>x_{c}</math> = 8000 Th).]]

	The sigmoid function <math>T_{m/z}</math> (ii) is a special type of a [https://en.wikipedia.org/wiki/Generalised_logistic_function generalized logistic function], which is defined by the following equation:		The sigmoid function <math>T_{m/z}</math> (ii) is a special type of a [https://en.wikipedia.org/wiki/Generalised_logistic_function generalized logistic function], which is defined by the following equation:

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:14:58Z

Peak picking - basic concepts

← Older revision		Revision as of 16:14, 8 October 2025
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	:iii) the noise distribution function multiplied by a constant.		:iii) the noise distribution function multiplied by a constant.

	[[File:Threshold-for-peak-picking.jpg\|600px\|thumb\|right\| Sigmoidal function (ii) <math>T_{m/z}</math> used for peak picking. Note that the parameters indicated are used for illustration purposes and are generally not recommended for peak picking. The slope parameter ''l'' which equals 5.5 in this example (default is 7.5) defines the the slope of the curve at the x-position <math>x_{c}</math>. The latter parameter defines the point at which asymptote maximum (pos, or neg) growth occurs (in this example at 8000 Th).]]		[[File:Threshold-for-peak-picking.jpg\|600px\|thumb\|right\| Sigmoidal function (ii) <math>T_{m/z}</math> used for peak picking. Note that the parameters indicated are used for illustration purposes and are generally not recommended for peak picking. The slope parameter ''l'' which equals 5.5 in this example (default is 7.5) defines the the slope of the curve at the x-position <math>x_{c}</math>. The latter parameter defines the point at which asymptote maximum (pos, or neg) growth occurs (in this example at <math>x_{c}</math> = 8000 Th).]]

	The sigmoid function <math>T_{m/z}</math> (ii) is a special type of a [https://en.wikipedia.org/wiki/Generalised_logistic_function generalized logistic function], which is defined by the following equation:		The sigmoid function <math>T_{m/z}</math> (ii) is a special type of a [https://en.wikipedia.org/wiki/Generalised_logistic_function generalized logistic function], which is defined by the following equation:

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:13:52Z

Peak picking - basic concepts

← Older revision		Revision as of 16:13, 8 October 2025
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	:iii) the noise distribution function multiplied by a constant.		:iii) the noise distribution function multiplied by a constant.

	[[File:Threshold-for-peak-picking.jpg\|600px\|thumb\|right\| Sigmoidal function (ii) ~~''T(~~m/z~~)''~~ used for peak picking. Note that the parameters indicated are used for illustration purposes and are generally not recommended for peak picking. The ''slope'' parameter ''l'' which equals 5.5 in this example (default is 7.5) defines the the slope of the curve at the x-position ~~''m~~/~~z center''~~. The latter parameter defines the point at which asymptote maximum (pos, or neg) growth occurs (in this example at 8000 Th).]]		[[File:Threshold-for-peak-picking.jpg\|600px\|thumb\|right\| Sigmoidal function (ii) <math>T_{m/z}</math> used for peak picking. Note that the parameters indicated are used for illustration purposes and are generally not recommended for peak picking. The slope parameter ''l'' which equals 5.5 in this example (default is 7.5) defines the the slope of the curve at the x-position <math>x_{c}</math>. The latter parameter defines the point at which asymptote maximum (pos, or neg) growth occurs (in this example at 8000 Th).]]

	~~The sigmoid function (ii) is a special type of a [https://en.wikipedia.org/wiki/Generalised_logistic_function generalized logistic function], which is defined by the following equation:~~

			The sigmoid function <math>T_{m/z}</math> (ii) is a special type of a [https://en.wikipedia.org/wiki/Generalised_logistic_function generalized logistic function], which is defined by the following equation:

	::<math>T_{m/z} = {I_{m,s} \over (1+e^{k*(x-x_{c})})}</math> (1),		::<math>T_{m/z} = {I_{m,s} \over (1+e^{k*(x-x_{c})})}</math> (1),
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	To obtain the peak tables the intensity threshold function T(m/z) is automatically obtained on the basis of parameters indicated in the window ''peak pick parameters''. If the checkbox ''define number of peaks'' is not checked peak tables will contain only peaks with intensities larger than the threshold function. Otherwise the threshold function is scaled iteratively until the desired number of peaks is obtained.		To obtain the peak tables the intensity threshold function T(m/z) is automatically obtained on the basis of parameters indicated in the window ''peak pick parameters''. If the checkbox ''define number of peaks'' is not checked peak tables will contain only peaks with intensities larger than the threshold function. Otherwise the threshold function is scaled iteratively until the desired number of peaks is obtained.

	When peak picking is complete a peak table array is created with ''npeaks'' rows and ''four'' or ''six'' columns (npeaks is the number of peaks in the table, see below for a description of the contents of the peak table). Peak tables are automatically added to the corresponding MS spectra and are displayed in a list box on the left side of the MicrobeMS main window, below the list box with the ''MicrobeMS spectra IDs''. Note that existing peak tables may be overwritten without warning when new peak tables are created. Some computational details of the peak picking routine are available from the command line window if the ''peak pick verbose mode'' check box has been selected.		When peak picking is complete a peak table array is created with ''npeaks'' rows and ''four'' or ''six'' columns (''npeaks'' is the number of peaks in the table, see below for a description of the contents of the peak table). Peak tables are automatically added to the corresponding MS spectra and are displayed in a list box on the left side of the MicrobeMS main window, below the list box with the ''MicrobeMS spectra IDs''. Note that existing peak tables may be overwritten without warning when new peak tables are created. Some computational details of the peak picking routine are available from the command line window if the ''peak pick verbose mode'' check box has been selected.

	== Peak picking - the procedure ==		== Peak picking - the procedure ==

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:11:14Z

Peak picking - basic concepts

← Older revision		Revision as of 16:11, 8 October 2025
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	::<math>T(m/z) = {I_{m,s} \over (1+e^{k*(x-x_{c})})}</math> (1),		::<math>T_{m/z} = {I_{m,s} \over (1+e^{k*(x-x_{c})})}</math> (1),

	where		where
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	{\|		{\|
	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>T(m/z)</math>		\|<math>T_{m/z}</math>
	\|the intensity threshold function, i.e. the S-shaped sigmoid function according to (ii)		\|the intensity threshold function, i.e. the S-shaped sigmoid function according to (ii)
	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"

Laschp: /* Peak picking - basic concepts */

2025-10-08T14:10:23Z

Peak picking - basic concepts

← Older revision		Revision as of 16:10, 8 October 2025
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	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>l</math>		\|<math>l</math>
	\|(slope), affects the slope of the threshold function around ''x(c)''		\|slope, affects the slope of the threshold function around <math>x_{c}</math>
			\|- style="vertical-align:top;"
			\|<math>x_{c}</math>
			\|'center' of the sigmoidal function, denotes the x-position at which asymptote maximum (pos, or neg) growth occurs
	\|- style="vertical-align:top;"		\|- style="vertical-align:top;"
	\|<math>x</math>		\|<math>x</math>
	\|the x-vector (in Th units) ranging from mzlow to mzhigh (2000 - 13000 Th per default)		\|the x-vector (in Th units) ranging from mzlow to mzhigh (2000 - 13000 Th per default)
	~~\|- style="vertical-align:top;"~~
	~~\|<math>x_{c}</math>~~
	~~\|'center' of the sigmoidal function, denotes the x-position at which asymptote maximum (pos, or neg) growth occurs~~
	\|}		\|}