Convert sequences from one annotation style to another

Source: R/convertAnnotation.R

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`).

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

Arguments

x

Character vector with peptide sequences in ProForma format

convertToStyle

Character string specifying target format. Options: "deltaMass", "unimodId", "name"

massTolerance

Numeric mass tolerance in Daltons for matching modifications (default: 0.01). Used when converting from deltaMass.

verbose

`logical(1)`. If `FALSE`, warnings about unrecognised modifications are silenced (default: `TRUE`).

Value

Character vector with the sequences in the target annotation format

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"

Author

Guillaume Deflandre <guillaume.deflandre@uclouvain.be>

Examples

# Convert sequence from name to delta mass
convertAnnotation("M[Oxidation]PEPTIDE", convertToStyle = "deltaMass")
#> [1] "M[+15.994915]PEPTIDE"
# Result: "M[+15.994915]PEPTIDE"

# Name to Unimod ID
convertAnnotation("M[Oxidation]PEPTIDE", convertToStyle = "unimodId")
#> [1] "M[UNIMOD:35]PEPTIDE"
# Result: "M[UNIMOD:35]PEPTIDE"

# Delta mass to name
convertAnnotation("M[+15.995]PEPTIDE", convertToStyle = "name")
#> [1] "M[Oxidation]PEPTIDE"
# Result: "M[Oxidation]PEPTIDE"

# Multiple modifications
convertAnnotation("M[Oxidation]EVNES[Phospho]PEK", convertToStyle = "deltaMass")
#> [1] "M[+15.994915]EVNES[+79.966331]PEK"
# 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")
#> [1] "M[+15.994915]PEPTIDE" "EVNES[+79.966331]PEK" "PEPTIDE"             
# 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")
#> [1] "M[Oxidation]PEPTIDE" "S[Phospho]EQUENCE"  
# Result: c("M[Oxidation]PEPTIDE", "S[Phospho]EQUENCE")

# Convert to Unimod IDs
sequences <- c("M[Oxidation]PEPTIDE", "C[Carbamidomethyl]PEPTIDE")
convertAnnotation(sequences, convertToStyle = "unimodId")
#> [1] "M[UNIMOD:35]PEPTIDE" "C[UNIMOD:4]PEPTIDE" 
# Result: c("M[UNIMOD:35]PEPTIDE", "C[UNIMOD:4]PEPTIDE")