Documentation 
Calculate highresolution isotope mass distribution and density function
[MD, Info, DF]
= isotopicdist(SeqAA)
[MD, Info, DF]
= isotopicdist(Compound)
[MD, Info, DF]
= isotopicdist(Formula)
isotopicdist(..., 'NTerminal', NTerminalValue,
...)
isotopicdist(..., 'CTerminal', CTerminalValue,
...)
isotopicdist(..., 'Resolution', ResolutionValue,
...)
isotopicdist(..., 'FFTResolution', FFTResolutionValue,
...)
isotopicdist(..., 'FFTRange', FFTRangeValue,
...)
isotopicdist(..., 'FFTLocation', FFTLocationValue,
...)
isotopicdist(..., 'NoiseThreshold', NoiseThresholdValue,
...)
isotopicdist(..., 'ShowPlot', ShowPlotValue,
...)
[MD, Info, DF] = isotopicdist(SeqAA) analyzes a peptide sequence and returns a matrix containing the expected mass distribution; a structure containing the monoisotopic mass, average mass, most abundant mass, nominal mass, and empirical formula; and a matrix containing the expected density function.
[MD, Info, DF] = isotopicdist(Compound) analyzes a compound specified by a numeric vector or matrix.
[MD, Info, DF] = isotopicdist(Formula) analyzes a compound specified by an empirical chemical formula represented by the structure Formula. The field names in Formula must be valid element symbols and are case sensitive. The respective values in Formula are the number of atoms for each element. Formula can also be an array of structures that specifies multiple formulas. The field names can be in any order within a structure. However, if there are multiple structures, the order must be the same in each.
isotopicdist(..., 'PropertyName', PropertyValue, ...) calls isotopicdist with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Enclose each PropertyName in single quotation marks. Each PropertyName is case insensitive. These property name/property value pairs are as follows:
isotopicdist(..., 'NTerminal', NTerminalValue,
...) modifies the Nterminal of the peptide.
isotopicdist(..., 'CTerminal', CTerminalValue, ...) modifies the Cterminal of the peptide.
isotopicdist(..., 'Resolution', ResolutionValue, ...) specifies the approximate resolution of the instrument, given as the Gaussian width (in daltons) at full width at half height (FWHH).
isotopicdist(..., 'FFTResolution', FFTResolutionValue, ...) specifies the number of data points per dalton, to compute the fast Fourier transform (FFT) algorithm.
isotopicdist(..., 'FFTRange', FFTRangeValue, ...) specifies the absolute range (window size) in daltons for the FFT algorithm and output density function.
isotopicdist(..., 'FFTLocation', FFTLocationValue, ...) specifies the location of the FFT range (window) defined by FFTRangeValue. It specifies this location by setting the location of the lower limit of the range, relative to the location of the monoisotopic peak, which is computed by isotopicdist.
isotopicdist(..., 'NoiseThreshold', NoiseThresholdValue, ...) removes points in the mass distribution that are smaller than 1/NoiseThresholdValue times the most abundant mass.
isotopicdist(..., 'ShowPlot', ShowPlotValue, ...) controls the display of a plot of the mass distribution.
SeqAA 
Peptide sequence specified by either a:
 
Compound 
Compound specified by either a:
 
Formula 
Chemical formula specified by either a:
 
NTerminalValue 
Modification for the Nterminal of the peptide, specified by either:
 
CTerminalValue 
Modification for the Cterminal of the peptide, specified by either:
 
ResolutionValue 
Value in daltons specifying the approximate resolution of the instrument, given as the Gaussian width at full width half height (FWHH). Default: 1/16 Da  
FFTResolutionValue 
Value specifying the number of data points per dalton, used to compute the FFT algorithm. Default: 1000  
FFTRangeValue 
Value specifying the absolute range (window size) in daltons for the FFT algorithm and output density function. By default, this value is automatically estimated based on the weight of the molecule. The actual FFT range used internally by isotopicdist is further increased such that FFTRangeValue * FFTResolutionValue is a power of two.  
FFTLocationValue 
Fraction that specifies the location of the FFT range (window) defined by FFTRangeValue. It specifies this location by setting the location of the lower limit of the FFT range, relative to the location of the monoisotopic peak, which is computed by isotopicdist. The location of the lower limit of the FFT range is set to the mass of the monoistopic peak  (FFTLocationValue * FFTRangeValue).
Default: 1/16  
NoiseThresholdValue 
Value that removes points in the mass distribution that are smaller than 1/NoiseThresholdValue times the most abundant mass. Default: 1e6  
ShowPlotValue 
Controls the display of a plot of the isotopic mass distribution. Choices are true, false, or I, which is an integer specifying a compound. If set to true, the first compound is plotted. Default is:

Calculate and display the isotopic mass distribution of the peptide sequence MATLAP with an Acetyl Nterminal and an Amide Cterminal:
MD = isotopicdist('MATLAP','nterm','Acetyl','cterm','Amide', ... 'showplot',true) MD = 643.3363 0.6676 644.3388 0.2306 645.3378 0.0797 646.3386 0.0181 647.3396 0.0033 648.3409 0.0005 649.3423 0.0001 650.3439 0.0000 651.3455 0.0000
Calculate and display the isotopic mass distribution of Glutamine (C_{5}H_{10}N_{2}O_{3}):
MD = isotopicdist([5 10 2 3 0],'showplot',true) MD = 146.0691 0.9328 147.0715 0.0595 148.0733 0.0074 149.0755 0.0004 150.0774 0.0000
Display the isotopic mass distribution of the "averagine" model, whose molecular formula represents the statistical occurrences of amino acids from all known proteins:
isotopicdist([4.9384 7.7583 1.3577 1.4773 0.0417])
[1] Rockwood, A. L., Van Orden, S. L., and Smith, R. D. (1995). Rapid Calculation of Isotope Distributions. Anal. Chem. 67:15, 2699–2704.
[2] Rockwood, A. L., Van Orden, S. L., and Smith, R. D. (1996). Ultrahigh Resolution Isotope Distribution Calculations. Rapid Commun. Mass Spectrum 10, 54–59.
[3] Senko, M.W., Beu, S. C., and McLafferty, F. W. (1995). Automated assignment of charge states from resolved isotopic peaks for multiply charged ions. J. Am. Soc. Mass Spectrom. 6, 52–56.
[4] Senko, M.W., Beu, S. C., and McLafferty, F. W. (1995). Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6, 229–233.
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