convert_proforma: Convert a proforma string to a PTM object

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

Convert a proforma string to a PTM object

Description

Converts proforma strings to a PTM object that get_matched_peaks uses to calculate fragmentation patterns. If there is no modification annotation, the cleaned sequence is returned.

Usage

convert_proforma(proforma, AlternativeGlossary = NULL)

Arguments

proforma	A string written in the format "M.S[Methyl]S[22]S[23].V"
AlternativeGlossary	Try a different glossary. See system.file("extdata", "Unimod_v20220602.csv", package = "pspecterlib) for formatting.

Author(s)

Degnan, David. Flores, Javier.

Examples

## Not run: 

convert_proforma("M.(S)[Acetyl]ATNNIAQARKLVEQLRIEAGIERIKVSKAASDLMSYCEQHARNDPLLVGVPASENPFKDK(KPCIIL)[-52.9879].")

convert_proforma("M.SS[Methyl]S.V")

convert_proforma("M.S[Methyl]S[22]S[23].V")

convert_proforma("TESTTESTTEST")


## End(Not run)

EMSL-Computing/pspecterlib documentation built on Jan. 28, 2024, 8:13 p.m.