| Type: | Package |
| Title: | Mass Spectrometry Tools |
| Version: | 1.4.8 |
| Author: | Yonghui Dong |
| Maintainer: | Yonghui Dong <yonghui.dong@gmail.com> |
| Description: | Common mass spectrometry tools described in John Roboz (2013) <doi:10.1201/b15436>. It allows checking element isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks, examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) ion sources. |
| Depends: | R (≥ 3.5.0) |
| Imports: | stringr, crayon, xml2, stats |
| License: | GPL-2 |
| URL: | https://github.com/YonghuiDong/MSbox |
| BugReports: | https://github.com/YonghuiDong/MSbox/issues/new |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.2 |
| NeedsCompilation: | no |
| Packaged: | 2022-12-08 14:22:36 UTC; dong |
| Repository: | CRAN |
| Date/Publication: | 2022-12-08 14:42:31 UTC |
Element isotopes
Description
check element isotope information
Usage
E_iso(S)
Arguments
S |
element, can be element symbol (i.e. C) or full name (i.e. Carbon). Both Element symbol and full name are case insensitive. |
Author(s)
Yonghui Dong
Examples
E_iso('Na') # element symbol
E_iso('nA') # element symbol, case insensitive
E_iso('Carbon') # element full name
E_iso('carBon') # element full name, case insensitive
Isotope labelled molecular mass
Description
Calculate isotope labelled molecular mass
Usage
Iso_mass(F, iso)
Arguments
F |
chemical formula, case insensitive |
iso |
labelled elements, case insensitive |
Author(s)
Yonghui Dong
Examples
Iso_mass(F = 'C7H6O4', iso = '[13]C2[2]H3') # Two 13C and three 2H are labled
Isotope labelled molecular mass
Description
Calculate isotope labelled m/z
Usage
Iso_mz(F, iso, z)
Arguments
F |
chemical formula, case insensitive |
iso |
labelled elements, case insensitive |
z |
charge |
Author(s)
Yonghui Dong
Examples
Iso_mz(F = 'C7H6O4', iso = '[13]C2[2]H3', z = -1) # Two 13C and three 2H are labled
Common adducts
Description
calculate common adduct ions in positive or negative ion mode
Usage
adduct(F, mode = c("+", "-"))
Arguments
F |
chemical formula, case insensitive |
mode |
ionization mode, either positive '+' or negative '-' |
Author(s)
Yonghui Dong
Examples
adduct('C1H4', mode = '-')
adduct('C1h4', mode = '+')
Contaminants in MS
Description
check the possible contaminants
Usage
contam(mz, mode = NULL, ppm = 10)
Arguments
mz |
suspected m/z value |
mode |
ionization mode, either positive '+' or negative '-' |
ppm |
mass tolerance, default value = 10 |
Author(s)
Yonghui Dong
Examples
contam(33.0335, ppm = 10, mode = '+')
contam(44.998, ppm = 10, mode = '-')
Get the compound information
Description
get compound formula and structure from https://cactus.nci.nih.gov/chemical/structure
Usage
describe(chem, representation = "formula", info = FALSE)
Arguments
chem |
chemical name of the compound |
representation |
representation methods, formula is default |
info |
extra molecular information that users can query |
Author(s)
Yonghui Dong
Examples
## Not run:
describe('malic acid', "formula")
describe(c('malic acid', 'citric acid', 'tartaric acid'), "smiles")
## End(Not run)
Performing statistics
Description
performing statistics, including calculating fold change, p-values and VIP values
Usage
doStat(x, Group = NULL)
Arguments
x |
sample ion intensity matrix, row sample, column feature. |
Group |
sample group information |
Value
a dataframe with statistical information
Examples
dat <- matrix(runif(2*300), ncol = 2, nrow = 300)
rownames(dat) <- 1:dim(dat)[1]
myGroup <- rep_len(LETTERS[1:3], 300)
ret <- doStat(dat, Group = myGroup)
Calculate coefficient of variation (CV)
Description
Calculate coefficient of variation (CV), also known as relative standard deviation (RSD) among different sample groups
Usage
getCV(x, Group = NULL)
Arguments
x |
sample ion intensity matrix, row sample, column feature. |
Group |
sample group information |
Value
a dataframe with mean values and cv
Examples
dat <- matrix(runif(2*300), ncol = 2, nrow = 300)
myGroup <- rep_len(LETTERS[1:2], 300)
ret <- getCV(dat, Group = myGroup)
calculate fold change
Description
calculate fold change among different samples.
Usage
getFC(x, Group = NULL)
Arguments
x |
sample ion intensity matrix, row sample, column feature. |
Group |
sample group information |
Value
a dataframe with mean values and fold changes
Examples
dat <- matrix(runif(2*300), ncol = 2, nrow = 300)
myGroup <- rep_len(LETTERS[1:2], 300)
ret <- getFC(dat, Group = myGroup)
Get the sample name which has the max ion intensity
Description
get the sample name which has the max ion intensity
Usage
getMax(x)
Arguments
x |
sample ion intensity matrix, row sample, column feature. |
Value
a data frame
Examples
dat <- cbind.data.frame(mz = c(100, 101, 300), mz2 = c(0, 0 , 1), mz3 = c(1, 9, 1))
rownames(dat) <- c("A", "B", "C")
out <- getMax(dat)
get p-values
Description
get p-values from Post Hoc analysis
Usage
getP(x, Group = NULL)
Arguments
x |
sample ion intensity matrix, row sample, column feature. |
Group |
sample group information |
Value
a data frame
Examples
dat <- matrix(runif(2*300), ncol = 2, nrow = 300)
myGroup <- rep_len(LETTERS[1:3], 300)
out <- getP(dat, Group = myGroup)
molecular mass
Description
calculate accurate molecular mass
Usage
mass(F, caseSensitive = FALSE)
Arguments
F |
chemical formula, case insensitive |
caseSensitive |
if case sensitive is 'FALSE' (default), the elements are seperated by numbers. for instance, Carbon dioxyde can be written as 'c1o2' or any combination of the two elements in lower or upper cases. However, the number of elements should be clearly stated in the chemical formula. if case sensitive is 'TRUE', the elements are seperated by upper case letters. For instance, Carbon dioxyde must be written as 'C1O2' or ‘CO2'. You don’t meed to write the number of the element if it is 1. |
Author(s)
Yonghui Dong
Examples
mass('C7h7o1')
mass('C7H7O', caseSensitive = TRUE)
mass(c('C7H7O4', 'C'), caseSensitive = TRUE) # vector input
mass(c('c7h7O4', 'c1'))
Calculate accurate mass-to-charge ratio
Description
Calculate accurate mass-to-charge ratio (m/z)
Usage
mz(m, z, caseSensitive = FALSE)
Arguments
m |
chemical formula of an ion, case insensitive |
z |
charge |
caseSensitive |
if case sensitive is 'FALSE' (default), the elements are seperated by numbers. for instance, Carbon dioxyde can be written as 'c1o2' or any combination of the two elements in lower or upper cases. However, the number of elements should be clearly stated in the chemical formula. if case sensitive is 'TRUE', the elements are seperated by upper case letters. For instance, Carbon dioxyde must be written as 'C1O2' or ‘CO2'. You don’t meed to write the number of the element if it is 1. |
Author(s)
Yonghui Dong
Examples
mz('C7h7o1', z = 1)
mz('C7H7O', z = 1, caseSensitive = TRUE)
mz(c('C7H7O4', 'C'), z = -1, caseSensitive = TRUE) # vector input
mz(c('c7h7O4', 'c1'), z = -1)
mass accuracy
Description
calculate the mass accuracy of measured m/z. lazy input allowed
Usage
ppm(m, t, lazy = TRUE)
Arguments
m |
measured m/z |
t |
theoretical m/z |
lazy |
if lazy input is allowed |
Author(s)
Yonghui Dong
Examples
ppm(155.03383, 155.03388) # with m/z value
ppm(155.03383, .03388) # lazy input when the integer parts of m and t are the same
ppm(155.03384, mz('C7H7O4', z = 1)) # with ion formula
Search in customized database
Description
search in customized database based on accurate m/z and RT
Usage
searchDB(DF, DB, ppm = 5, RT = 0.2, useRT = FALSE)
Arguments
DF |
input file, should contain at least a column named mz |
DB |
database, should contain at least a column named mz |
ppm |
mass tolerance, default 5ppm |
RT |
retention time tolerance, default 0.2min |
useRT |
should RT be considered during database search? |
Author(s)
Yonghui Dong
Examples
DF <- cbind.data.frame(mz = c(100.001, 100.1), RT = c(10, 11))
DB <- cbind.data.frame(mz = c(100.001, 100.1), RT = c(10, 12.1))
searchDB(DF, DB, ppm = 5, RT = 0.2, useRT = TRUE)
search for m/z in from the idiom metabolomics database
Description
tentative metabolite identification based on m/z value search
Usage
what(myMZ, mode = NULL, ppm = 5, useDB = "HMDB")
Arguments
myMZ |
m/z values |
mode |
ionization mode, either positive '+' or negative '-' |
ppm |
mass tolerance, default value = 10 |
useDB |
which database to use, HMDB or KEGG? default is HMDB |
Author(s)
Yonghui Dong
Examples
a = what(133.014, mode = '-', ppm = 10)