isotopicdist
Calculate highresolution isotope mass distribution and density function
Syntax
[
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
,
...)
Description
[
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(SeqAA
)
[
analyzes
a compound specified by a numeric vector or matrix. MD
, Info
, DF
]
= isotopicdist(Compound
)
[
analyzes
a compound specified by an empirical chemical formula represented
by the structure MD
, Info
, DF
]
= isotopicdist(Formula
)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(..., '
calls PropertyName
', PropertyValue
,
...)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',
modifies the Nterminal of the peptide.NTerminalValue
,
...)
isotopicdist(..., 'CTerminal',
modifies the Cterminal of the peptide.CTerminalValue
,
...)
isotopicdist(..., 'Resolution',
specifies the approximate resolution of the instrument,
given as the Gaussian width (in daltons) at full width at half height
(FWHH).ResolutionValue
,
...)
isotopicdist(..., 'FFTResolution',
specifies the number of data points per dalton, to
compute the fast Fourier transform (FFT) algorithm.FFTResolutionValue
,
...)
isotopicdist(..., 'FFTRange',
specifies the absolute range (window size) in daltons
for the FFT algorithm and output density function.FFTRangeValue
,
...)
isotopicdist(..., 'FFTLocation',
specifies the location of the FFT range (window)
defined by FFTLocationValue
,
...)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',
removes points in the mass distribution that are
smaller than NoiseThresholdValue
,
...)1/
times
the most abundant mass.NoiseThresholdValue
isotopicdist(..., 'ShowPlot',
controls the display of a plot of the mass distribution.ShowPlotValue
,
...)
Input Arguments

Peptide sequence specified by either a:
Tip You can use the 

Compound specified by either a:


Chemical formula specified by either a:
Note If 

Modification for the Nterminal of the peptide, specified by either:


Modification for the Cterminal of the peptide, specified by either:


Value in daltons specifying the approximate resolution of the instrument, given as the Gaussian width at full width half height (FWHH). Default: 

Value specifying the number of data points per dalton, used to compute the FFT algorithm. Default: 

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 Tip Increase the Tip Ultrahigh resolution allows you to resolve micropeaks that have
the same nominal mass, but slightly different exact masses. To achieve
ultrahigh resolution, increase 

Fraction that specifies the location of the FFT range (window)
defined by Tip You may need to shift the FFT range to the left in rare cases where a compound contains an element, such as Iron or Argon, whose most abundant isotope is not the lightest one. Default: 

Value that removes points in the mass distribution that are
smaller than Default: 

Controls the display of a plot of the isotopic mass distribution.
Choices are

Output Arguments

Mass distribution represented by a twocolumn matrix in which each row corresponds to an isotope. The first column lists the isotopic mass, and the second column lists the probability for that mass. 

Structure containing mass information for the peptide sequence or compound in the following fields:


Density function represented by a twocolumn matrix in which each row corresponds to an m/z value. The first column lists the mass, and the second column lists the relative intensity of the signal at that mass. 
Examples
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])
More About
References
[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.
Version History
See Also
cleave
 getgenpept
 genpeptread
 int2aa
 nt2aa
 aminolookup
 cleavelookup
 molweight