| Title: | Efficient Calculation of Fine Structure Isotope Patterns via Fourier Transforms of Simplex-Based Elemental Models |
|---|---|
| Description: | Provides a function that quickly computes the fine structure isotope patterns of a set of chemical formulas to a given degree of accuracy (up to the limit set by errors in floating point arithmetic). A data-set comprising the masses and isotopic abundances of individual elements is also provided and calculation of isotopic gross structures is also supported. |
| Authors: | Andreas Ipsen |
| Maintainer: | Andreas Ipsen <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.1 |
| Built: | 2024-11-28 06:33:57 UTC |
| Source: | CRAN |
Provides a function that quickly computes the fine structure isotope patterns of a set of chemical formulas to a given degree of accuracy (up to the limit set by errors in floating point arithmetic). A data-set comprising the masses and isotopic abundances of individual elements is also provided and calculation of isotopic gross structures is also supported.
| Package: | ecipex |
| Type: | Package |
| Version: | 1.1 |
| Date: | 2020-03-12 |
| License: | GPL (>= 2) |
| LazyLoad: | true |
Andreas Ipsen
This function can calculate either the fine structure isotope patterns or the gross structure isotope patterns for a given set of chemical formulas. It returns the isotope patterns as a list of data frames which may be sorted by mass or abundance.
ecipex(formulas, isoinfo = ecipex::nistiso, limit = 1e-12, id = FALSE, sortby = "abundance", gross = FALSE, groupby = "mass")ecipex(formulas, isoinfo = ecipex::nistiso, limit = 1e-12, id = FALSE, sortby = "abundance", gross = FALSE, groupby = "mass")
formulas |
a character vector specifying the
chemical formulas whose isotope patterns are to be
calculated. The elements specified must be present in
|
isoinfo |
a data frame that specifies the masses and
isotopic abundances of the elements to be used in the
calculations. Must include the variables |
limit |
isotopologues with abundances below this value are ignored. |
id |
determines whether the full isotopic
composition of each isotopic variant should be specified
in the output. Setting this to |
sortby |
should be one of |
gross |
if |
groupby |
determines how the fine structure
isotope patterns are grouped together when the gross structure
isotope patterns are calculated. If it is equal to |
The fine structure isotope pattern of each formula is calculated by
applying the multi-dimensional fast Fourier transform to
a simplex-based representation of each element's isotopic
abundance. The algorithm is most efficient when the atom
counts of the same elements in different formulas are
roughly similar. Performance can also be improved by
increasing limit although this should be done with
care. It is generally not advisable to reduce
limit below its default value, as this can
increase memory requirements significantly and is
unlikely to provide information of any value, since the
natural isotopic abundances can be quite variable. If gross
is set to TRUE then the gross structure isotope patterns
are calculated directly from the fine structure isotope patterns.
Note that for centroids with extremely low abundances (say less than
one billionth of the total) the centroided masses
can be somewhat inaccurate due to floating point errors.
A list of data frames containing the fine structure
isotope patterns of each formula in formulas. The
list names are determined by formulas, so that the
isotope pattern of any given formula is easily extracted.
If id is set to TRUE, the output will
include additional columns listing the counts of each
distinct isotope of each element. If gross
is set to TRUE, the output will instead contain the
gross structure isotope patterns of each formula in formulas.
Ipsen, A., Efficient Calculation of Exact Fine Structure Isotope Patterns via the Multidimensional Fourier Transform, Anal. Chem., 2014, 86 (11), pp 5316-5322
http://pubs.acs.org/doi/abs/10.1021/ac500108n
# a simple molecule iso_H2O <- ecipex("H2O")[[1]] iso_H2O # reduce limit for larger molecule and sort output by mass iso_C254H338N65O75S6 <- ecipex("C254H338N65O75S6", limit=1e-8, sortby="mass")[[1]] head(iso_C254H338N65O75S6) # check that sum of all abundances is still close to 1 sum(iso_C254H338N65O75S6$abundance) # inspect the full isotope pattern, the fine structure, and the full pattern on a log scale par(mfrow=c(1,3)) plot(iso_C254H338N65O75S6, t="h") plot(iso_C254H338N65O75S6, t="h", xlim=c(5691.29, 5691.31)) plot(iso_C254H338N65O75S6, t="h", log="y") # calculate isotopic abundances with enriched Carbon-13 modifiediso <- nistiso modifiediso[modifiediso$element=="C",3] <- c(0.9, 0.1) ecipex("C2", isoinfo=modifiediso) # the isotope pattern can be calculated quickly if the elements only have 2 stable isotopes system.time(iso_C10000H10000 <- ecipex("C10000H10000", limit=1e-8)[[1]]) # this is typically a more demanding calculation because S has 4 stable isotopes system.time(iso_S50 <- ecipex("S50", limit=1e-8)[[1]]) # if the limit is greater than the most abundant isotopologue the output is uninformative iso_C10000H10000_useless <- ecipex("C10000H10000", limit=0.015) # calculate the isotope patterns of multiple formulas, and include the detailed isotopic composition multisopatterns <- ecipex(c("H2O", "CO2", "O2", "C8H18", "C60"), sortby="mass", id=TRUE) # inspect C8H18 in particular multisopatterns$C8H18 # make sure all abundances are close to 1 sapply(multisopatterns, function(x){sum(x$abundance)}) # due to floating point errors, the following are not identical iso_C60_almostComplete <- ecipex("C60", limit= 0)[[1]] iso_C60_reallyComplete <- ecipex("C60", limit= -1)[[1]] # the latter includes negative isotopic abundances because the floating point errors are orders of # magnitude greater than the "true" abundances. The variations in natural isotopic abundances will # typically be much greater than floating point errors. # calculate the gross structure isotope pattern, grouping the fine structure isotopologues by mass ecipex("C6H14N4O2", sortby="mass", gross=TRUE, groupby="mass")# a simple molecule iso_H2O <- ecipex("H2O")[[1]] iso_H2O # reduce limit for larger molecule and sort output by mass iso_C254H338N65O75S6 <- ecipex("C254H338N65O75S6", limit=1e-8, sortby="mass")[[1]] head(iso_C254H338N65O75S6) # check that sum of all abundances is still close to 1 sum(iso_C254H338N65O75S6$abundance) # inspect the full isotope pattern, the fine structure, and the full pattern on a log scale par(mfrow=c(1,3)) plot(iso_C254H338N65O75S6, t="h") plot(iso_C254H338N65O75S6, t="h", xlim=c(5691.29, 5691.31)) plot(iso_C254H338N65O75S6, t="h", log="y") # calculate isotopic abundances with enriched Carbon-13 modifiediso <- nistiso modifiediso[modifiediso$element=="C",3] <- c(0.9, 0.1) ecipex("C2", isoinfo=modifiediso) # the isotope pattern can be calculated quickly if the elements only have 2 stable isotopes system.time(iso_C10000H10000 <- ecipex("C10000H10000", limit=1e-8)[[1]]) # this is typically a more demanding calculation because S has 4 stable isotopes system.time(iso_S50 <- ecipex("S50", limit=1e-8)[[1]]) # if the limit is greater than the most abundant isotopologue the output is uninformative iso_C10000H10000_useless <- ecipex("C10000H10000", limit=0.015) # calculate the isotope patterns of multiple formulas, and include the detailed isotopic composition multisopatterns <- ecipex(c("H2O", "CO2", "O2", "C8H18", "C60"), sortby="mass", id=TRUE) # inspect C8H18 in particular multisopatterns$C8H18 # make sure all abundances are close to 1 sapply(multisopatterns, function(x){sum(x$abundance)}) # due to floating point errors, the following are not identical iso_C60_almostComplete <- ecipex("C60", limit= 0)[[1]] iso_C60_reallyComplete <- ecipex("C60", limit= -1)[[1]] # the latter includes negative isotopic abundances because the floating point errors are orders of # magnitude greater than the "true" abundances. The variations in natural isotopic abundances will # typically be much greater than floating point errors. # calculate the gross structure isotope pattern, grouping the fine structure isotopologues by mass ecipex("C6H14N4O2", sortby="mass", gross=TRUE, groupby="mass")
A data frame giving the masses, standard isotopic
abundances and nucleon numbers of most chemical elements
as provided by the Physical Measurement Laboratory of the
National Institute of Standards and Technology (but taken
from separate publications). It includes the four
variables element (the chemical symbol),
mass, abundance and nucleons,
arranged so that each isotope is uniquely specified by
one row.
http://www.nist.gov/pml/data/comp.cfm