Package 'massSpectrometryR'

Description

custom operator for subtracting formulas from one another, to make calculating with formulas a little more clear

Usage

formula1 %f-% formula2

Arguments

Examples

c(H = 2, O = 1) %f-% c(H = 1)
c(H = 2, O = 1) %f-% c(S = 1, O = 2)

Description

custom operator for adding up formulas, to make calculating with formulas a little more clear

Usage

formula1 %f+% formula2

Arguments

Examples

waterFormula() %f+% protonFormula()
waterFormula() %f+% c(C=1, O = 2)
c(H = 2, O = 1) %f+% c(S = 1, O = 2)

Description

Adding up two formulas, taking into account possible differing elements

Usage

addFormulas(formula1, formula2)

Arguments

Value

a named numeric vector (formula)

Examples

addFormulas(waterFormula(), protonFormula())
addFormulas(waterFormula(), c(C=1, O=2))

Description

Take a list of formulas and adds them all up

Usage

addListFormulas(formulas)

Arguments

Value

a named numeric vector (formula)

Examples

addListFormulas(list(c(H = 2, O = 1),
                     c(H = 1),
                     c(H = 2, O = 1),
                     c(S = 1, O = 2)))

Description

R6 Class representing a set of amino acids. It adds three functions to quickly switch between different writing 'styles' of peptides

Details

Note: this class is meant to be used only for amino acids and such

Super class

massSpectrometryR::chemicals -> aminoacids

Methods

Public methods

• aminoAcidClass$getName()

• aminoAcidClass$getShort()

• aminoAcidClass$translatePeptide()

• aminoAcidClass$clone()

Method getName()

Function to retrieve the full name of an amino acid via the letter or shorts

Usage

aminoAcidClass$getName(searchString, checkCase = TRUE)

Arguments

Returns

character vector, name of the aminoacid

Method getShort()

Function to retrieve either the 1- or 3- letter code of an amino acid

Usage

aminoAcidClass$getShort(searchString, checkCase = TRUE)

Arguments

Returns

character vector, 1- or 3- letter code of the aminoacid

Method translatePeptide()

Translates a amino acid sequence from 1-letter codes to 3-letter codes and vice versa

Usage

aminoAcidClass$translatePeptide(
  sequence,
  from1to3 = FALSE,
  splitCharacter = NA,
  joinCharacter = NA,
  checkCase = TRUE
)

Arguments

Returns

character vector, sequence in either 1- or 3-letter codes

Method clone()

The objects of this class are cloneable with this method.

Usage

aminoAcidClass$clone(deep = FALSE)

Arguments

Examples

aminoAcidResidues()$getShort("L")
aminoAcidResidues()$getShort("Leu")
aminoAcidResidues()$getName("L")
aminoAcidResidues()$getName("Leu")
aminoAcidResidues()$translatePeptide("Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu",
 from1to3 = TRUE, splitCharacter ="-")
aminoAcidResidues()$translatePeptide("DRVYIHPFHL", joinCharacter = "-")

Description

Returns a pre-defined object which contains info on some common amino acid modifications

Usage

aminoAcidModifications()

Value

An object of class modifications containing info on amino acid modifications

Note

the resulting modification table cannot be used immediately: there is two times a fixed modification for Cysteine amino acids. Remove one of them to prevent errors when using peptide calculations

Examples

print(aminoAcidModifications)

Description

Generates a pre-defined object which contains info on 'normal' amino acid residues

Usage

aminoAcidResidues()

Value

a R6 object of class 'chemicals'

Note

The formulas in the object are amino acid residues as they are present in proteins. To get the actual formula of the amino acid in its 'free' form, add c(H=2, O=1) (water)

this object is used in all protein calculations in this package

Examples

print(aminoAcidResidues())

Description

calculates the mass (Da) when it deviates a certain ppm (part per million) from the reference mass (Da).

Usage

calculate.Measured.mz(referenceMz, ppm)

Arguments

Value

a numeric vector

Examples

calculate.Measured.mz(465.6025, 5)
calculate.Measured.mz(465.6025, 0)
calculate.Measured.mz(465.6025, -5)

Description

calculates the mass deviation in ppm (parts per million) between the measured mass or m/z and a reference mass or m/z (both in Da).

Usage

calculate.ppm(referenceMz, measuredMz)

Arguments

Value

a numeric vector

Examples

calculate.ppm(465.6025, 465.6028)
calculate.ppm(465.6025, 465.6025)
calculate.ppm(465.6025, 465.7025)

Description

calculate the reference mass (Da) from a maesured mass (Da) which deviates a certain amount (ppm). Somewhat odd calculation, that is usually not needed in the lab, but is sometimes needed in theoretical situations or in programming.

Usage

calculate.Reference.mz(measuredMz, ppm)

Arguments

Value

a numeric vector

Examples

calculate.ppm(465.6025, 465.6028)
calculate.Measured.mz(465.6025, 0.644)
calculate.Reference.mz(465.6028, 0.644)

Description

Every chemical inside the object has a name, letter, short and a formula. The first 3 can be any length of string (though the letter and short field should be maximum length (nchar) 1 and 2-4 respectively). Formula should be in the form of a named numeric with the names representing elements and the values themselves being the number of atoms of that element, eg c(C = 3, H = 5, N = 1, O = 1, S = 0)

Details

Note: this class is meant to be used for classes of compounds, eg amino acids

Also: his class is meant as a base class to be expanded via inheritance

Warning: all chemicals inside this object should be unique (names, letters & shorts)

Active bindings

Methods

Public methods

• chemicals$new()

• chemicals$print()

• chemicals$getFormula()

• chemicals$clone()

Method new()

Create a new chemicals object

Usage

chemicals$new(letters, shorts, names, formulas)

Arguments

Returns

a new 'chemical' object

Method print()

For printing purposes: prints a table of the chemicals with columns letter, name & short

Usage

chemicals$print(...)

Arguments

Method getFormula()

Retrieves the formula of one of the compounds in the object

Usage

chemicals$getFormula(which1)

Arguments

Returns

a formula in the shape of a named numeric vector, eg c(C = 6, H = 12, N = 4, O = 1, S = 0)

Method clone()

The objects of this class are cloneable with this method.

Usage

chemicals$clone(deep = FALSE)

Arguments

Examples

estrogens <- chemicals$new(letters = c("1","2","3","4"),
                           shorts = c("E1","E2","E3","E4"),
                           names = c("Estrone","Estradiol",
                                     "Estriol","Estetrol"),
                           formulas = list(c(C=18, H=22, O=2),
                                           c(C=18, H=24, O=2),
                                           c(C=18, H=24, O=3),
                                           c(C=18, H=24, O=4)))

Description

Digests a sequence and returns

Usage

digest(sequence, enzyme = "trypsin", missed = 0)

Arguments

Value

data.frame with the columns 'peptide', 'start', 'stop' and 'mc' (missed cleavages)

Note

This function is an modified version of the Digest function found in the package 'OrgMassSpecR'

Description

generates a pre-defined formula for electron

Usage

electronFormula()

Value

a named numeric vector (formula)

Note

this is used for calculations

Examples

print(electronFormula())

Description

Every element inside the object has a name, letter and a mass. The first 2 can be any length of string, mass should be a numeric

Details

Note: this class is meant to be used for elements.

Warning: all elements inside this object should be unique (names & shorts, not mass)

Active bindings

Methods

Public methods

• elements$new()

• elements$addElement()

• elements$print()

• elements$getMass()

• elements$clone()

Method new()

creates a new elements object

Usage

elements$new(shorts, names, mass)

Arguments

Returns

a new 'elements' object

Method addElement()

adds one or more elements to the object. Elements to be added must have unique names and shorts.

Usage

elements$addElement(shorts, names, mass)

Arguments

Returns

nothing

Method print()

For printing purposes: prints a table of the chemicals with columns letter, name & short

Usage

elements$print(...)

Arguments

Method getMass()

Retrieves the mass of one of the elements in the object

Usage

elements$getMass(which1)

Arguments

Returns

a numeric value

Method clone()

The objects of this class are cloneable with this method.

Usage

elements$clone(deep = FALSE)

Arguments

Examples

randomElements <- elements$new(shorts = c("X1","X2","X3"),
                               names  = c("Secret Element 1",
                                          "Secret Element 2",
                                          "Secret Element 1"),
                               mass   = c(301, 312, 323))

Description

generates a pre-defined object which contains info on elements, mass values are average masses (weighted mean mass of elements based on their natural occurence)

Usage

elementsAverage()

Value

an elements object

Note

electron is not really meant to be used in formulas, but is needed to calculate mass & m/z of ions

Examples

print(elementsAverage())

Description

retrieves the names of the elements in a formula

Usage

elementsInFormula(formula, removeZero = FALSE)

Arguments

Value

character vector

Examples

glucose = c(C=6, H=12, O=6, S=0)
elementsInFormula(glucose)
elementsInFormula(glucose, removeZero = TRUE)

Description

especially important when formula1 contains elements that formula2 does not contain and vice versa, Note: also sorts the result

Usage

elementsInFormulas(formula1, formula2, decrease = FALSE)

Arguments

Value

a character vector

Examples

elementsInFormulas(c(O = 2, C = 1),
                   c(H = 2, S = 1))

Description

generates a pre-defined R6 elements object which contains info on elements, mass values are mono isotopic

Usage

elementsMonoisotopic()

Value

an elements object

Note

this object is (by default) used in all chemical calculations in this package

electron is not really meant to be used in formulas, but is needed to calculate mass & m/z of ions

Examples

print(elementsMonoisotopic())

Description

generates an empty pre-defined formula

Usage

emptyFormula()

Value

a named numeric vector (formula)

Note

this can be used for calculations and setup of unknowns

Examples

print(emptyFormula())

Description

Translates regular formula format into a character vector, eg C6H12O6

Usage

formulaString(formula, removeSingle = FALSE, useMarkdown = FALSE)

Arguments

Value

character vector

Examples

formulaString(c(C=6, H=12, O=6))
formulaString(c(H=3,O=4,P=1))
formulaString(c(H=3,O=4,P=1), removeSingle = TRUE)
formulaString(c(H=2, O=1))
formulaString(c(H=2, O=1), removeSingle = TRUE)

Description

calculates the neutral mono-isotopic mass of a formula

Usage

formulaToMass(
  formula = NULL,
  removeNA = FALSE,
  elementsInfo = elementsMonoisotopic(),
  enviPat = FALSE,
  exact = TRUE
)

Arguments

Value

numeric vector

Examples

formulaToMass(c(H=2, O=1))
formulaToMass(c(H=2, O=1), elementsInfo = elementsAverage())
formulaToMass(c(C = 50, H=102))
formulaToMass(c(C = 50, H=102), elementsInfo = elementsAverage())
formulaToMass(c(C = 50, H=102), enviPat = TRUE)
formulaToMass(c(C = 50, H=102), enviPat = TRUE, exact = FALSE)

Description

Calculates the m/z value of a charged/adducted ion

Usage

massToMz(
  mass,
  adducts = 0,
  adductFormula = electronFormula(),
  adductCharge = -1,
  elementsInfo = elementsMonoisotopic(),
  enviPat = FALSE,
  exact = TRUE
)

Arguments

Value

numeric vector

Examples

# amino acid residue lysine + water
lysineMass <- formulaToMass(aminoAcidResidues()$getFormula("K") %f+% waterFormula())
lysineMass
# M+H+ : adducts =  1, adductFormula = protonFormula(), adductCharge = 1
# singly charged/protonated ion (ESI)
massToMz(lysineMass,
         adducts = 1,
         adductFormula = protonFormula(),
         adductCharge = 1)
# Doubly charged/protonated ion (ESI)
massToMz(lysineMass,
         adducts = 2,
         adductFormula = protonFormula(),
         adductCharge = 1)
# M-H- : single, negatively charged
massToMz(lysineMass,
         adducts = -1,
         adductFormula = protonFormula(),
         adductCharge = 1)
# M+ : singly positively charged (molecular) ion (EI)
massToMz(lysineMass,
         adducts = -1,
         adductFormula = electronFormula(),
         adductCharge = 1)
# M- : singly negatively charged (molecular) ion (EI)
massToMz(lysineMass,
         adducts = 1,
         adductFormula = electronFormula(),
         adductCharge = 1)

Description

a wrapper around massToMz for positively charged, protonated ions in ESI

Usage

massToMzH(
  mass,
  charge = 1,
  elementsInfo = elementsMonoisotopic(),
  enviPat = FALSE,
  exact = TRUE
)

Arguments

Value

numeric vector

Examples

# amino acid residue lysine + water
lysineMass <- formulaToMass(aminoAcidResidues()$getFormula("K") %f+% waterFormula())
lysineMass
# M+H+ : adducts =  1, adductFormula = protonFormula(), adductCharge = 1
# singly charged/protonated ion (ESI)
massToMz(lysineMass,
         adducts = 1,
         adductFormula = protonFormula(),
         adductCharge = 1)
massToMzH(lysineMass)

Description

Every modification inside the object has a name, position, fixed (flag), gain (formula), loss (formula) and category.

'name' is a character vector.

Position is a character vector specifying the amino acids which always have the modification (fixed = TRUE) or can have the modification (fixed = FALSE). More than one amino acid can be specified, eg NQ (for Asparagine & glutamine). Please note that currently the package does NOT support 'exotic' amino acids (eg Selenocysteine) or 'combination' letters, such as 'J' (Leucine or Isoleucine). For the C- and N-terminus, use 'C_Term' or 'N_Term' for position.

Gain and loss specify what is lost and/or gained when a amino acid is modified. For example Carbamidomethylation of Cysteine has both a loss formula c(H=1) and a gain formula c(C=2, H=4, N=1, O=1); obviously this could also be defined as: loss formula = emptyFormula(), gain formula = c(C=2, H=3, N=1, O=1).

For the category field (character vector) there is no real 'rule' on how to classify modifications. I usually stick to the categorisation of Mascot or Sequest.

Active bindings

Methods

Public methods

• modifications$new()

• modifications$print()

• modifications$add()

• modifications$addTable()

• modifications$clone()

Method new()

Create a new modifications object

Usage

modifications$new(data = NA)

Arguments

Method print()

For printing purposes: prints a table of the modifications

Usage

modifications$print(...)

Arguments

Method add()

Adds a single modification

Usage

modifications$add(name, position, fixed, gain, loss, category)

Arguments

Returns

nothing

Method addTable()

Add (a set of) modifications via a tibble

Usage

modifications$addTable(data = NA)

Arguments

Returns

nothing

Method clone()

The objects of this class are cloneable with this method.

Usage

modifications$clone(deep = FALSE)

Arguments

Note

the logical vector fixed is very important. If TRUE, then a modification is considered to be always present, if FALSE then its presence is optional.

Examples

aaModifications <- modifications$new()
aaModifications$addTable(
  tibble::tibble(
    name = c("Carbamidomethyl (C)",
             "Carboxymethyl (C)",
             "Oxidation (M)"),
    position = c("C","C","M"),
    fixed = c(TRUE,TRUE,FALSE),
    gain = list(c(C = 2, H = 4, N = 1, O = 1),
                c(C = 2, H = 3, N = 0, O = 2),
                c(C = 0, H = 0, N = 0, O = 1)),
    loss = list(c(protonFormula()),
                c(protonFormula()),
                c(emptyFormula())),
    category = c("Cys-state","Cys-state","Preparation Artefact")
  )
)
aaModifications
aaModifications$add(name = "Deamidation",
                    position = "NQ",
                    fixed = FALSE,
                    gain = c(O = 1, H = 1),
                    loss = c(N = 1, H =2),
                    category = "Preparation Artefact")
aaModifications

Description

a wrapper around mzToMass for positively charged, protonated ions in ESI

Usage

mzHToMass(
  mz,
  charge = 1,
  elementsInfo = elementsMonoisotopic(),
  enviPat = FALSE,
  exact = TRUE
)

Arguments

Value

numeric vector

Examples

massToMzH(mass = 174.1117, charge = 2) |> mzHToMass(charge = 2)
 massToMzH(mass = 174.1117, charge = 1) |> mzHToMass(charge = 1)

Description

essentially the reverse of the massToMz

Usage

mzToMass(
  mz,
  adducts = 0,
  adductFormula = electronFormula(),
  adductCharge = -1,
  elementsInfo = elementsMonoisotopic(),
  enviPat = FALSE,
  exact = TRUE
)

Arguments

Value

numeric vector

Examples

massToMz(mass = 174.1117, adductFormula = c(e=1), adducts = 2, adductCharge = -1) |>
 mzToMass(adductFormula = c(e=1), adducts = 2, adductCharge = -1)
massToMz(mass = 174.1117, adductFormula = c(H=1), adducts = 1, adductCharge = 1) |>
 mzToMass(adductFormula = c(H=1), adducts = 1, adductCharge = 1)

Description

translates a proteome Discoverer (Thermo Scientific) elements formula string to a formula as used by this package

Usage

pdToFormula(pdFormula)

Arguments

Value

formula of format c(H=2, O=1)

Examples

glucose <- pdToFormula("C(6) H(12) O(6)")
glucose
water <- pdToFormula("H(2) O")
water

Description

Contains two character vectors: one representing the amino acid sequence, and a second conatining info on the positions of 'variable' modifications. The object also contains a modification table specifying the 'fixed' amd 'variable' modifications.

Active bindings

Methods

Public methods

• peptide$new()

• peptide$print()

• peptide$sequence.part()

• peptide$modifications.part()

• peptide$modifications.formula.part()

• peptide$modifications.formula()

• peptide$formula.part()

• peptide$formula()

• peptide$mass.part()

• peptide$mass()

• peptide$mz.part()

• peptide$mz()

• peptide$mzH.part()

• peptide$mzH()

• peptide$fragments.part()

• peptide$fragments()

• peptide$fragments.part.immoniumIons()

• peptide$fragments.immoniumIons()

• peptide$clone()

Method new()

Create a new peptide object

Usage

peptide$new(sequence = "", modificationTable = NA, variableModifications = NA)

Arguments

Returns

a new 'peptide' object

Method print()

For printing purposes: prints the sequence string, the variable modifications string and the modification table

Usage

peptide$print(...)

Arguments

Method sequence.part()

Retrieve part of the amino acid squence. Note: intended for internal use

Usage

peptide$sequence.part(startSeq = 1L, endSeq = 1L)

Arguments

Returns

character vector

Method modifications.part()

Retrieve part of the variable modification string. Note: intended for internal use

Usage

peptide$modifications.part(startSeq = 1L, endSeq = 1L)

Arguments

Returns

character vector

Method modifications.formula.part()

Determines the gain & loss formulas for a part of the peptide (waviable modification string and modification table are used for this): adds up all the losses and gains. If the position of a variable modification in the variable modification string does not match the amino acid in the modification table, then a warning is produced

Usage

peptide$modifications.formula.part(
  startSeq = 1L,
  endSeq = 1L,
  Nterminal = TRUE,
  Cterminal = TRUE
)

Arguments

Returns

a list of 2 formulas: the summed up gain formulas & the summed up loss formulas which are present in the part selected by startSeq and endSeq)

Method modifications.formula()

Deterines the gain & loss formulas for the full length of the peptide sequence. Essentially a wrapper for modifications.formula.part

Usage

peptide$modifications.formula(Nterminal = TRUE, Cterminal = TRUE)

Arguments

Returns

a list of 2 formulas: the summed up gain formulas & the summed up loss formulas which are present in the part selected by startSeq and endSeq)

Method formula.part()

Determines the chemical formula of part of the peptide with or without the modifications.

Usage

peptide$formula.part(
  startSeq = 1,
  endSeq = 1,
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE
)

Arguments

Returns

a named numeric vector, eg: c(C=6, H=12, O=6)

Method formula()

Determines the chemical formula of the full length peptide with or without modifications. Essentially a wrapper around 'formula.part'

Usage

peptide$formula(
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE
)

Arguments

Returns

a named numeric vector, eg: c(C=6, H=12, O=6)

Method mass.part()

Calculate the mass of part of the peptide with or without modifications

Usage

peptide$mass.part(
  startSeq = 1,
  endSeq = 1,
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE,
  elementsInfo = elementsMonoisotopic()
)

Arguments

Returns

numeric vector

Method mass()

Calculate the mass of the full length peptide with or without modifications

Usage

peptide$mass(
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE,
  elementsInfo = elementsMonoisotopic()
)

Arguments

Returns

numeric vector

Method mz.part()

Calculate the m/z of part of the peptide (as an ion) with or without modifications

Usage

peptide$mz.part(
  startSeq = 1,
  endSeq = 1,
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE,
  elementsInfo = elementsMonoisotopic(),
  adducts = 1,
  adductFormula = protonFormula(),
  adductCharge = 1
)

Arguments

Returns

numeric vector

Method mz()

Calculate the m/z of the full length peptide (as an ion) with or without modifications

Usage

peptide$mz(
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE,
  elementsInfo = elementsMonoisotopic(),
  adducts = 1,
  adductFormula = protonFormula(),
  adductCharge = 1
)

Arguments

Returns

numeric vector

Method mzH.part()

Calculate the m/z of part of the peptide (as a protonated ion) with or without modifications

Usage

peptide$mzH.part(
  startSeq = 1,
  endSeq = 1,
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE,
  charge = 1,
  elementsInfo = elementsMonoisotopic()
)

Arguments

Returns

numeric vector

Method mzH()

Calculate the m/z of part of the peptide (as a protonated ion) with or without modifications

Usage

peptide$mzH(
  charge = 1,
  ignoreModifications = FALSE,
  Nterminal = TRUE,
  Cterminal = TRUE,
  elementsInfo = elementsMonoisotopic()
)

Arguments

Returns

numeric vector

Method fragments.part()

generates a table of fragments which could arise from fragmenting part of the peptide. The ionseries generated are: a, a-H2O, a-NH3, b, b-H2O, b-NH3, b+H2O, c, x, y, y-H2O, y-NH3, z. Please note that the calculation is relatively 'dumb': it does NOT check whether a fragment is possible at all. Prime example is the B+H2O ion series: these fragment ions can only if certain conditions are met. Currently there is no check in this function that checks these conditions/assumptions

Usage

peptide$fragments.part(
  startSeq = 1,
  endSeq = 1,
  ignoreModifications = FALSE,
  onlyIons = TRUE,
  chargeState = 1,
  returnFormulas = FALSE,
  formulaIncludeChargeProtons = FALSE
)

Arguments

Returns

a data.frame with fragment information

Method fragments()

generates a table of fragments which could arise from fragmenting the full sequence of the peptide. The ion series generated are: a, a-H2O, a-NH3, b, b-H2O, b-NH3, b+H2O, c, x, y, y-H2O, y-NH3, z. Please note that the calculation is relatively 'dumb': it does NOT check whether a fragment is possible at all. Prime example is the B+H2O ion series: these fragment ions can only if certain conditions are met. Currently there is no check in this function that checks these conditions/assumptions

Usage

peptide$fragments(
  ignoreModifications = FALSE,
  onlyIons = TRUE,
  chargeState = 1,
  returnFormulas = FALSE,
  formulaIncludeChargeProtons = FALSE
)

Arguments

Returns

a data.frame with fragment information

Method fragments.part.immoniumIons()

generates a numeric vector containing 'expected' immonium ions based on the amino acid content of part of the peptide. Please note that this function does NOT take into account possible (fixed or variable) modifications

Usage

peptide$fragments.part.immoniumIons(startSeq = 1, endSeq = 1)

Arguments

Returns

numeric vector

Method fragments.immoniumIons()

generates a numeric vector containing 'expected' immonium ions based on the amino acid content of the full sequence of the peptide. Please note that this function does NOT take into account possible (fixed or variable) modifications

Usage

peptide$fragments.immoniumIons()

Returns

numeric vector

Method clone()

The objects of this class are cloneable with this method.

Usage

peptide$clone(deep = FALSE)

Arguments

Examples

testPeptide <- peptide$new(sequence = "SAMPLER",
                           modificationTable = aminoAcidModifications()$table,
                           variableModifications = "0010000")
testPeptide
testPeptide$formula()

Description

counts the occurence of a amino acid (sequence) in another amino acid sequence

Usage

peptideCount(
  thePeptide = NA,
  searchPeptide = NA,
  doNotSplice = TRUE,
  upper = TRUE
)

Arguments

Value

numeric vector

Examples

peptideCount("SAMPLER", "P")
peptideCount("SAMPLER", "PLER", doNotSplice = TRUE)
peptideCount("SAMPLER", "PLER", doNotSplice = FALSE)

Description

gives formula of a peptide string

Usage

peptideFormula(peptide, aminoAcids = aminoAcidResidues())

Arguments

Value

a numeric vector

Note

does not check for non-amino acid letters, modifications cannot be specified

Examples

peptideFormula("SAMPLER")

Description

Generates a pre-defined (incomplete) table of names of fragments for the ions resulting when fragmenting a peptide in MS

Usage

peptideFragments()

Value

a data.frame of two columns: 'name' and 'series name' of fragments

Note

will possibly be removed in the future

Description

gives ion m/z of the protonated peptide

Usage

peptideMzH(
  peptide,
  charge = 1,
  aminoAcids = aminoAcidResidues(),
  elementsInfo = elementsMonoisotopic()
)

Arguments

Value

a numeric vector

Note

does not check for non-amino acid letters, modifications cannot be specified

Examples

peptideMzH("SAMPLER")
peptideMzH("SAMPLER", charge = 2)
peptideMzH("SAMPLER", elementsInfo = elementsAverage())

Description

generates a pre-defined formula for proton

Usage

protonFormula()

Value

a named numeric vector (formula)

Examples

print(protonFormula())

Description

translates an cdkFormula object to a 'regular' formula format

Usage

rcdkFormula(cdkformula)

Arguments

Value

formula of format c(H=2, O=1)

Note

This function does not deal with the charge state which is possibly defined in the rcdkFormula object

Examples

glucose <- rcdk::get.formula("C6H12O6")
rcdkFormula(glucose)
glucoseAdductIon <- rcdk::get.formula("C6H12O6Na1", charge = 1)
glucoseAdductIon
# to get to the same m/z value
glucoseAdductIon |> massSpectrometryR::rcdkFormula() |> formulaToMass() |> massToMz(adducts = -1)

Description

removes elements that have number zero

Usage

removeZeros(formula)

Arguments

Value

named numeric vector (formula)

Examples

glucose = c(O=6, H=12, C=6)
glucose %f+% emptyFormula()
removeZeros(glucose %f+% emptyFormula())

Description

sorts the elements of a formula in alphabetical order (increasing/decreasing)

Usage

sortFormula(formula, decrease = FALSE)

Arguments

Value

named numeric vector (formula)

Examples

glucose = c(O=6, H=12, C=6)
glucose
sortFormula(glucose)

Description

Translates a character vector formula, eg 'C6H12O6' to a regular formula c(C=6, H=12, O=6)

Usage

stringFormula(string)

Arguments

Value

formula of format c(H=2, O=1)

Note

it's imperative that every element has a number (count), otherwise this function is highly likely to malfunction and return NA

Examples

stringFormula("H3O4P1")
stringFormula("C6H12O6")

Description

Translates a character vector formula, eg 'C6H12O6' to a regular formula c(C=6, H=12, O=6)

Usage

stringToFormula(string, removeCharacters = c("\\[", "\\]"))

Arguments

Value

formula of format c(H=2, O=1)

Note

this function is an improved version of stringFormula(). Now every elements with count 1 can have the number omitted. However, the function depends on 'correct' elements (first letter is uppercase, second letter is lowercase). This function also allows for the presence of isotopes, eg '[13]C' or '[2]H2O'

Examples

stringToFormula("H3O4P1")
stringToFormula("C6H12O6")
stringToFormula("C6H5Br")
stringToFormula("[13]C6H12O5[18]O")
stringToFormula("[13]C6H12O5[18]O", removeCharacters = NA)

Description

subtracting one formula from another, taking into account possible differing elements

Usage

subtractFormulas(formula1, formula2)

Arguments

Value

a named numeric vector (formula)

Note

There are no checks for negative values!

Examples

subtractFormulas(c(H = 2, O = 1), c(H = 1))
subtractFormulas(c(H = 2, O = 1), c(S = 1, O = 2))

Description

checks if formula is valid

Usage

validFormula(formula, string = FALSE)

Arguments

Value

logical vector

Note

This is done via the check_chemform function from the package enviPat

Examples

glucose <- c(C=6, H=12, O=6)
validFormula(glucose)
formulaString(glucose)
validFormula(formulaString(glucose), string = TRUE)

Description

generates a pre-defined formula for water

Usage

waterFormula()

Value

a named numeric vector (formula)

Examples

print(waterFormula())