Digest {OrgMassSpecR} | R Documentation |
Cleave an amino acid sequence (a protein or peptide) according to enzyme specific rules and calculate the precursor ion m/z values.
Digest(sequence, enzyme = "trypsin", missed = 0, IAA = TRUE, N15 = FALSE, custom = list())
sequence |
a character string representing the amino acid sequence to be cleaved by the enzyme. |
enzyme |
a character string specifying the rules for cleavage. Options are "trypsin" (default) or "pepsin" . |
missed |
the maximum number of missed cleavages. Must be an integer of 0 (default) or greater. An error will result if the specified number of missed cleavages is greater than the maximum possible number of missed cleavages. |
IAA |
logical. TRUE specifies iodoacetylated cysteine and FALSE specifies unmodified cystine. |
N15 |
logical indicating if the nitrogen-15 isotope should be used in place of the default nitrogen-14 isotope. |
custom |
a list specifying user defined residues as custom = list(code, mass) , where code is a vector of one letter characters and mass is a vector of the respective monoisotopic masses. See Details and Examples. |
The amino acid residues must be specified by one letter codes. The predefined residues are:
A = alanine | L = leucine |
R = arginine | K = lysine |
N = asparagine | M = methionine |
D = aspartic acid | F = phenylalanine |
C = cysteine | P = proline |
E = glutamic acid | S = serine |
Q = glutamine | T = threonine |
G = glycine | W = tryptophan |
H = histidine | Y = tyrosine |
I = isoleucine | V = valine |
If "trypsin"
is specified, the sequence is cleaved on the c-terminal side of K and R residues, except if K or R is followed by P. If "pepsin"
is specified, the sequence is cleaved on the c-terminal side of F, L, W, Y, A, E, and Q residues. This rule is specific to pepsin at pH > 2, as used in hydrogen-deuterium exchange experiments.
The argument IAA
specifies treatment of the protein with iodoacetamide. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S).
If TRUE
, the argument N15
specifies 100% nitrogen-15 incorporation. It is intended for proteins grown with a nitrogen-15 labeled food source. (Although the experiment itself may grow a protein with less than 100% nitrogen-15 incorporation). Setting N15 = TRUE
does not modify the mass of a custom residue, or the mass of the nitrogen(s) added if IAA = TRUE
.
If a custom residue code is identical to a predefined residue code, the custom residue mass will be used in place of the predefined mass.
The error message “object "mass" not found
” indicates the input sequence contains an undefined residue(s).
A data frame with the following column names.
peptide |
resulting peptides. |
start |
beginning residue positions in the the original sequence. |
end |
ending residue positions in the the original sequence. |
mc |
number of missed cleavages. |
mz1 |
monoisotopic m/z values for the [M + H]1+ ions (where M is the precursor mass) |
mz2 |
monoisotopic m/z values for the [M + 2H]2+ ions |
mz3 |
monoisotopic m/z values for the [M + 3H]3+ ions |
Nathan G. Dodder
The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.
MonoisotopicMass
, FragmentPeptide
## digest human serum albumin with 0 and 1 missed cleavages Digest(hsaSequence, missed = 1) ## digest human serum albumin with a phosphoserine at position 58 ## and all methionines oxidized modifiedHsaSequence <- strsplit(hsaSequence, split = "")[[1]] modifiedHsaSequence[58] <- "s" # insert code for phosphoserine modifiedHsaSequence <- paste(modifiedHsaSequence, collapse = "") Digest(modifiedHsaSequence, custom = list(code = c("s","M"), mass = c(MonoisotopicMass(list(C=3, H=6, N=1, O=5, P=1)), MonoisotopicMass(list(C=5, H=9, N=1, O=2, S=1)))))