Package 'PTMods'

Description

The 'PTMods' package focuses on handling post-translational modifications (PTMs). It distributes PTMs from the Unimod database and allows to convert PTM annotations between multiple formats.

Author(s)

Maintainer: Guillaume Deflandre [email protected] (ORCID)

Authors:

• Laurent Gatto [email protected] (ORCID)

• Sebastian Gibb [email protected] (ORCID)

References

https://github.com/RforMassSpectrometry/PTMods/

See Also

Useful links:

• https://github.com/RforMassSpectrometry/PTMods

• Report bugs at https://github.com/RforMassSpectrometry/PTMods/issues

Description

Applies fixed modifications to peptide sequences.

The annotation style of modifications already present in 'sequences' is preserved as-is. The annotation style of newly applied modifications matches the style supplied in 'fixedModifications': numeric values produce deltaMass notation (e.g. '[+79.966331]'), while character values are used verbatim (e.g. '[Phospho]' or '[UNIMOD:21]').

Usage

addFixedModifications(sequences, fixedModifications = c(C = 57.021464))

Arguments

  "ATK" |>
    addFixedModifications(c(T = "+57.024")) |>
    addFixedModifications(c(T = "Phospho"))

Value

A named list of character strings with all fixed modifications applied to the corresponding amino acids, one element per input sequence.

Author(s)

Guillaume Deflandre <[email protected]>

Examples

addFixedModifications("ATCK")
addFixedModifications("ATCK", fixedModifications = c(Nterm = 304, C = 57.02146))
addFixedModifications("ATSK", fixedModifications = c(A = -42, S = 79.966331))
addFixedModifications("ATK", fixedModifications = c(T = "Phospho", A = 42))
addFixedModifications("A[+42]TK", fixedModifications = c(T = "Phospho"))
addFixedModifications("AT[+79.966]AK", fixedModifications = c(A = 42))
addFixedModifications("ATA[+79.966]K", fixedModifications = c(A = 42))

## Apply two modifications to the same residue consecutively
"ATK" |>
    addFixedModifications(c(T = "+57.024")) |>
    addFixedModifications(c(T = "Phospho"))

Description

A convenience wrapper around [addFixedModifications()] and [addVariableModifications()] that applies both fixed and variable modifications in a single call. Fixed modifications are applied first, followed by the enumeration of all possible combinations of variable modifications. Optionally, the annotation style of the output can be converted via [convertAnnotation()].

Usage

addModifications(
  sequences,
  fixedModifications = NULL,
  variableModifications = NULL,
  convertToStyle = NULL,
  ...
)

Arguments

Value

A 'character' vector of peptidoforms. The length is greater than or equal to 'length(sequences)', as each input sequence may expand into multiple peptidoforms corresponding to all combinations of variable modifications.

Author(s)

Guillaume Deflandre <[email protected]>

See Also

* addFixedModifications for applying fixed modifications.

* addVariableModifications for enumerating variable modification combinations.

* convertAnnotation for converting between modification annotation styles.

Examples

## Fixed modifications only
addModifications(
    c("ATCK", "PEPCK"),
    fixedModifications = c(C = 57.02146)
)

## Variable modifications only
addModifications(
    c("ATSK", "PEPTSK"),
    variableModifications = c(S = 79.966331, T = 79.966331),
    maxMods = 2
)

## Both fixed and variable modifications
addModifications(
    "ATCSK",
    fixedModifications = c(C = 57.02146),
    variableModifications = c(S = 79.966331, T = 79.966331),
    maxMods = 1
)

## Return annotations in UniMod name style
addModifications(
    "ATSK",
    variableModifications = c(S = 79.966331, T = 79.966331),
    convertToStyle = "name"
)

## N-terminal fixed modification with variable modifications
addModifications(
    "ATSK",
    fixedModifications = c(Nterm = 304),
    variableModifications = c(S = 79.966331)
)

Description

Generates all possible combinations of variable modifications for peptide sequences.

The annotation style of modifications already present in 'sequences' is preserved as-is. The annotation style of newly applied modifications matches the style supplied in 'variableModifications': numeric values produce deltaMass notation (e.g. '[+79.966331]'), while character values are used verbatim (e.g. '[Phospho]' or '[UNIMOD:21]').

Usage

addVariableModifications(
  sequences,
  variableModifications = NULL,
  maxMods = Inf
)

Arguments

  seq |>
    addVariableModifications(c(T = "+57.024")) |>
    addVariableModifications(c(T = "Phospho"))

Value

A named list of character vectors with all possible combinations of modifications, one element per input sequence.

Author(s)

Guillaume Deflandre <[email protected]>

Examples

addVariableModifications(
    "APGHKA",
    variableModifications = c(A = 4, K = 5, S = 8),
    maxMods = 2
)
addVariableModifications(
    "APGHKA",
    variableModifications = c(A = 4, K = 5, S = 8),
    maxMods = 3
)
addVariableModifications(
    c("ATK", "PAK"),
    variableModifications = c(T = "Phospho", A = "UNIMOD:1")
)
addVariableModifications(
    "A[+10]KT[-5]",
    variableModifications = c(A = -20, T = "Phospho")
)

## Apply two modifications to the same residue consecutively
"ATK" |>
    addVariableModifications(c(T = "+57.024")) |>
    addVariableModifications(c(T = "Phospho"))

Description

'data.frame' of aminoacids from the unimod database.

Usage

data("aminoacids")

Format

A 'data.frame' with 11 columns (OneLetter, ThreeLetter, FullName, AvgMass, MonoMass, H, C, N, O S, Se) for the aminoacids. The H/C/N/O/S/Se columns contain the number of elements that build the aminoacid.

Details

It was created as follows:

“' PTMods:::.createDataSets() “'

Source

Taken from the unimod database: http://www.unimod.org/xml/unimod.xml.

Examples

data(aminoacids)
head(aminoacids)

Description

Combines consecutive modifications on amino acids in peptide sequences.

Usage

combineModifications(sequences)

Arguments

Value

A character vector of the same length as 'sequences' with consecutive modifications on each amino acid summed into a single modification. This summed modifications is written in delta mass format.

Author(s)

Guillaume Deflandre <[email protected]>

Examples

combineModifications("AT[+10][-5]K")
combineModifications("[+10]-[-5]-ATK")
combineModifications("AT[Phospho][UNIMOD:1]K")
combineModifications("EM[+15.9949][-10]EK[+42][-8]")
combineModifications(c("AT[+10][-5]K", "EM[+15.9949][-10]EK"))

Description

Converts modifications between different annotation formats for multiple sequences at once. See the details and examples sections for more information. The annotation styles are inferred from the 'modifications' dataframe (see '?modifications').

Usage

convertAnnotation(
  x,
  convertToStyle = c("deltaMass", "unimodId", "name"),
  massTolerance = 0.01,
  verbose = TRUE
)

Arguments

Details

The function handles three main conversion scenarios:

• Name to deltaMass: "M[Oxidation]PEPTIDE" -> "M[+15.994915]PEPTIDE"

• Name to unimodId: "M[Oxidation]PEPTIDE" -> "M[UNIMOD:35]PEPTIDE"

• deltaMass to name: "M[+15.995]PEPTIDE" -> "M[Oxidation]PEPTIDE"

• deltaMass to unimodId: "M[+15.995]PEPTIDE" -> "M[UNIMOD:35]PEPTIDE"

• unimodId to name: "M[UNIMOD:35]PEPTIDE" -> "M[Oxidation]PEPTIDE"

• unimodId to deltaMass: "M[UNIMOD:35]PEPTIDE" -> "M[+15.994915]PEPTIDE"

Value

Character vector with the sequences in the target annotation format

Author(s)

Guillaume Deflandre <[email protected]>

Examples

# Convert sequence from name to delta mass
convertAnnotation("M[Oxidation]PEPTIDE", convertToStyle = "deltaMass")
# Result: "M[+15.994915]PEPTIDE"

# Name to Unimod ID
convertAnnotation("M[Oxidation]PEPTIDE", convertToStyle = "unimodId")
# Result: "M[UNIMOD:35]PEPTIDE"

# Delta mass to name
convertAnnotation("M[+15.995]PEPTIDE", convertToStyle = "name")
# Result: "M[Oxidation]PEPTIDE"

# Multiple modifications
convertAnnotation("M[Oxidation]EVNES[Phospho]PEK", convertToStyle = "deltaMass")
# Result: "M[+15.994915]EVNES[+79.966331]PEK"

# Convert multiple sequences from name to delta mass
sequences <- c("M[Oxidation]PEPTIDE", "EVNES[Phospho]PEK", "PEPTIDE")
convertAnnotation(sequences, convertToStyle = "deltaMass")
# Result: c("M[+15.994915]PEPTIDE", "EVNES[+79.966331]PEK", "PEPTIDE")

# Convert from delta mass to name
sequences <- c("M[+15.995]PEPTIDE", "S[+79.966]EQUENCE")
convertAnnotation(sequences, convertToStyle = "name")
# Result: c("M[Oxidation]PEPTIDE", "S[Phospho]EQUENCE")

# Convert to Unimod IDs
sequences <- c("M[Oxidation]PEPTIDE", "C[Carbamidomethyl]PEPTIDE")
convertAnnotation(sequences, convertToStyle = "unimodId")
# Result: c("M[UNIMOD:35]PEPTIDE", "C[UNIMOD:4]PEPTIDE")

Description

'data.frame' of chemical elements from the unimod database.

Usage

data("elements")

Format

A 'data.frame' with 4 columns (Name, FullName, AvgMass, MonoMass) for the chemical elements.

Details

It was created as follows:

“' PTMods:::.createDataSets() “'

Source

Taken from the unimod database: http://www.unimod.org/xml/unimod.xml.

Examples

data(elements)
head(elements)

Description

Remove any modifications annotation on a sequence. Annotation from any type (so long as they are specified within brackets "[..]") are removed.

Usage

getCanonicalSequence(x)

Arguments

Value

'character', a 'character' vector with sequences cleaned of all modifications.

Examples

getCanonicalSequence(
    c(
        "EM[-15.9949]EVEES[+79.9663]PEK",
        "EK[Acetyl]EVEES[UNIMOD:21]PEK"
    )
)

Description

Given a character vector of peptide sequences containing modifications in any annotation style (deltaMass, UniMod ID, or name), returns a named integer vector with the count of each unique modification. Regardless of the input annotation style, all modifications are converted to their UniMod name in the output (e.g. '[+79.966]' and '[UNIMOD:21]' both appear as 'Phospho').

Usage

getModificationsCounts(sequences)

Arguments

Value

A named integer vector where names are UniMod modification names and values are their occurrence counts across all input sequences. Returns an empty integer vector if no modifications are found.

Author(s)

Guillaume Deflandre <[email protected]>

Examples

seqs <- c(
    "[+304]-AT[Phospho]K",
    "AC[Carbamidomethyl]T[+79.966]S[Phospho]K",
    "PEPTIDE"
)
getModificationsCounts(seqs)

Description

'data.frame' of modifications from the unimod database.

Usage

data("modifications")

Format

A 'data.frame' with 15 columns (Id (created by Name:(Position-)Site(:NeutralLoss) because unimod id is not unique), UnimodId, Name, Description, AvgMass, MonoMass, Site, Position, Classification, SpecGroup, NeutralLoss, LastModification, Approved, Hidden) for the modifications.

Details

It was created as follows:

“' PTMods:::.createDataSets() “'

Source

Taken from the unimod database: http://www.unimod.org/xml/unimod.xml.

Examples

data(modifications)
head(modifications)