artmsProtein2SiteConversion {artMS}R Documentation

Converts the Proteins column of the evidence file to site-specific Uniprot_PTM notation

Description

It enables the site-specific quantification of PTMs by converting the Proteins column of the evidence file to an Uniprot_PTM or RefSeq_PTM notation. In this way, each of the modified peptides can be quantified independently across conditions. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING: we have detected a version of MaxQuant (1.6.3.4) outputs a' "Modified sequence" column of the evidence file that has two important changes for the annotation of phosphorylation:

Usage

artmsProtein2SiteConversion(evidence_file, ref_proteome_file, output_file,
  mod_type, verbose = TRUE)

Arguments

evidence_file

(char) The evidence file name and location

ref_proteome_file

(char) The reference proteome used as database to search the evidence.txt file with MaxQuant. It will be used to map the modified peptide to the protein sequence and find the site location. Therefore, it does not use the MaxQuant's Phospho (STY)Sites.txt

output_file

(char) Output file name (-sites-evidence.txt recommended)

mod_type

(char) The posttranslational modification. Options:

  • UB: Protein Ubiquitination

  • PH: Protein Phosphorylation

  • AC: Protein Acetylation

verbose

(logical) TRUE (default) shows function messages

Value

(file) Return a new evidence file with the Proteins column modified by adding the sequence site location(s) + postranslational modification(s) to the uniprot entry / refseq id.

Examples: A34890_ph3; Q64890_ph24_ph456; Q64890_ub34_ub129_ub234; Q64890_ac35.

Examples

# Testing warning if files are not submitted
artmsProtein2SiteConversion(evidence_file = NULL, ref_proteome_file = NULL, 
output_file = NULL)

[Package artMS version 1.0.12 Index]