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Included more metabolic labelling options #53

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Included more metabolic labelling options #53

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952271f
Updated function for more options of metabolic labelling ('13c' and '…
Jan 23, 2024
a78c5b2
Enabled calculation of average labelled peptide mass. Corrected the c…
Jan 23, 2024
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70 changes: 60 additions & 10 deletions R/massShift.R
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Original file line number Diff line number Diff line change
Expand Up @@ -11,17 +11,17 @@
#'
#' \itemize{
#' \item silac_13c
#' \href{http://www.unimod.org/modifications_view.php?editid1=188}{Unimod 188}
#' \href{https://www.unimod.org/modifications_view.php?editid1=188}{Unimod 188}
#'
#' \item silac_13c15n
#' \href{http://www.unimod.org/modifications_view.php?editid1=259}{Unimod 259} and
#' \href{http://www.unimod.org/modifications_view.php?editid1=267}{Unimod 267}
#' \href{https://www.unimod.org/modifications_view.php?editid1=259}{Unimod 259} and
#' \href{https://www.unimod.org/modifications_view.php?editid1=267}{Unimod 267}
#'
#' \item 15n
#' \href{http://www.unimod.org/modifications_view.php?editid1=994}{Unimod 994},
#' \href{http://www.unimod.org/modifications_view.php?editid1=995}{Unimod 995},
#' \href{http://www.unimod.org/modifications_view.php?editid1=996}{Unimod 996} and
#' \href{http://www.unimod.org/modifications_view.php?editid1=897}{Unimod 897}
#' \href{https://www.unimod.org/modifications_view.php?editid1=994}{Unimod 994},
#' \href{https://www.unimod.org/modifications_view.php?editid1=995}{Unimod 995},
#' \href{https://www.unimod.org/modifications_view.php?editid1=996}{Unimod 996} and
#' \href{https://www.unimod.org/modifications_view.php?editid1=897}{Unimod 897}
#'
#' }
#' @examples
Expand All @@ -34,8 +34,8 @@ function(seq, label = "none", aaShift = NULL, monoisotopic = TRUE){

# Check inputs
label <- tolower(label) # Renders case-insensitive input string.
if(!(label %in% c("none", "silac_13c", "silac_13c15n", "15n"))){
stop("Given label type unknown. Please use one of 'none', '15N', 'Silac_13C15N', or 'Silac_13C' (case-insensitive).")
if(!(label %in% c("none", "silac_13c", "silac_13c15n", "15n", "13c", "13c15n"))){
stop("Given label type unknown. Please use one of 'none', '15N', '13C', '13C15N', 'Silac_13C15N', or 'Silac_13C' (case-insensitive).")
}
if(!is.null(aaShift) & is.null(names(aaShift))){
stop("'aaShift' must be given as a named vector, e.g. 'aaShift = c(K = 6.020129)'.")
Expand Down Expand Up @@ -74,7 +74,57 @@ function(seq, label = "none", aaShift = NULL, monoisotopic = TRUE){
W = 2,
Y = 1,
V = 1
) * 0.997035 -0.003635*!monoisotopic # 0.997035 equals the mass shift from 14N to 15N. 0.9934 equals the average mass shift.
) * (0.997035 -0.003635*!monoisotopic) # 0.997035 equals the mass shift from 14N to 15N. 0.9934 equals the mass shift from average N to 15N.
} else if(label == "13c"){
aaShift <- c(
# U = ,
# O = ,
A = 3,
R = 6,
N = 4,
D = 4,
C = 3,
E = 5,
Q = 5,
G = 2,
H = 6,
I = 6,
L = 6,
K = 6,
M = 5,
F = 9,
P = 5,
S = 3,
T = 4,
W = 11,
Y = 9,
V = 5
) * (1.003355 -0.010705*!monoisotopic) # 1.003355 equals the mass shift from 12C to 13C. 0.99265 equals the mass shift from average C to 13C.
} else if(label == "13c15n"){
n <- 0.997035 -0.003635*!monoisotopic
c <- 1.003355 -0.010705*!monoisotopic
aaShift <- c(
A = 1*n + 3*c,
R = 4*n + 6*c,
N = 2*n + 4*c,
D = 1*n + 4*c,
C = 1*n + 3*c,
E = 1*n + 5*c,
Q = 2*n + 5*c,
G = 1*n + 2*c,
H = 3*n + 6*c,
I = 1*n + 6*c,
L = 1*n + 6*c,
K = 2*n + 6*c,
M = 1*n + 5*c,
F = 1*n + 9*c,
P = 1*n + 5*c,
S = 1*n + 3*c,
T = 1*n + 4*c,
W = 2*n + 11*c,
Y = 1*n + 9*c,
V = 1*n + 5*c
)
}

# Split sequence by amino acids
Expand Down
14 changes: 13 additions & 1 deletion tests/testthat/test.massShift.R
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,12 @@ test_that("massShift function: the computed value is wrong",{
test_that("massShift function: the computed value is wrong",{
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "15n"), expected = 14.95552, tolerance = 0.001)
})
test_that("massShift function: the computed value is wrong",{
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "13c"), expected = 47.15769, tolerance = 0.001)
})
test_that("massShift function: the computed value is wrong",{
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "13c15n"), expected = 62.11321, tolerance = 0.001)
})

# CHECK SHIFT VALUE - PREDEFINED LABELS - AVERAGE
test_that("massShift function: the computed value is wrong",{
Expand All @@ -27,7 +33,13 @@ test_that("massShift function: the computed value is wrong",{
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "silac_13c15n", monoisotopic = F), expected = 17.8723, tolerance = 0.001)
})
test_that("massShift function: the computed value is wrong",{
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "15n", monoisotopic = F), expected = 14.91554, tolerance = 0.001)
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "15n", monoisotopic = F), expected = 14.901, tolerance = 0.001)
})
test_that("massShift function: the computed value is wrong",{
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "13c", monoisotopic = F), expected = 46.65455, tolerance = 0.001)
})
test_that("massShift function: the computed value is wrong",{
expect_equal(object = massShift(seq = "AGEPKLDAGVR", label = "13c15n", monoisotopic = F), expected = 61.55555, tolerance = 0.001)
})

# CHECK OUTPUT CLASS
Expand Down