psm_to_peptide_style_modifications: Transformes PSM-level Modifications annotation style to...
In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data
View source: R/modifications.R
psm_to_peptide_style_modifications R Documentation
Transformes PSM-level Modifications annotation style to peptide-level style
Description
Proteome Discoverer has a different style of annotation for
peptide modifications in PSM and peptide-level outputs. In PSM-level output,
each modification is listed separately, with the modification in parentheses
after the position. In peptide-level output, the modifications are summarised
more succintly, with the number of each modification followed by the positions
For example:
PSM: N-Term(Prot)(Acetyl); C2(Carbamidomethyl); C16(Carbamidomethyl)
Peptide:1xAcetyl [N-Term]; 2xCarbamidomethyl [C2; C16]
Usage
psm_to_peptide_style_modifications(psm_style_modifications)
Arguments
psm_style_modifications
vector of PSM-style modification annotations
Value
vector of Peptide-style modification annotations
Examples
psm_mod <- "N-Term(Prot)(Acetyl); C2(Carbamidomethyl); C16(Carbamidomethyl)"
target <- "1xAcetyl [N-Term]; 2xCarbamidomethyl [C2; C16]"
psm_to_peptide_style_modifications(psm_mod) == target
CambridgeCentreForProteomics/camprotR documentation built on Jan. 27, 2023, 8:36 p.m.
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View source: R/modifications.R
| psm_to_peptide_style_modifications | R Documentation |
Transformes PSM-level Modifications annotation style to peptide-level style
Description
Proteome Discoverer has a different style of annotation for peptide modifications in PSM and peptide-level outputs. In PSM-level output, each modification is listed separately, with the modification in parentheses after the position. In peptide-level output, the modifications are summarised more succintly, with the number of each modification followed by the positions For example: PSM: N-Term(Prot)(Acetyl); C2(Carbamidomethyl); C16(Carbamidomethyl) Peptide:1xAcetyl [N-Term]; 2xCarbamidomethyl [C2; C16]
Usage
psm_to_peptide_style_modifications(psm_style_modifications)
Arguments
psm_style_modifications |
|
Value
vector of Peptide-style modification annotations
Examples
psm_mod <- "N-Term(Prot)(Acetyl); C2(Carbamidomethyl); C16(Carbamidomethyl)" target <- "1xAcetyl [N-Term]; 2xCarbamidomethyl [C2; C16]" psm_to_peptide_style_modifications(psm_mod) == target
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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