Converts the Protein ID column of the evidence file selected by the user to mod-site-specific notation: ProteinID to ProteinID_AAnumber notation

Source: R/protein2SiteConversion.R

It enables the modified-peptide specific quantification by converting the Protein column of the evidence file selected by the user to an ProteinID_AAnumbernotation. In this way, each of the modified peptides can be quantified independently across conditions.

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WARNING: we have detected a version of MaxQuant (>1.6.3.0) outputs a` "Modified sequence" column of the evidence file that has two important changes for the annotation of phosphorylation:

  • Uses p instead of (ph)

  • The modified residue (i.e. STY) is the residue on the right of the p, instead of the residue to the left of (ph), as usual. We have introduced a modification to detect and address this issue, but we advice the user to double check both the new evidence file with the introduce new notation and the -mapping.txt file and check that there are no NA values for the notation of phophopeptides.

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artmsProtein2SiteConversion(
  evidence_file,
  ref_proteome_file,
  column_name = c("Leading razor protein", "Leading proteins", "Proteins"),
  output_file,
  mod_type,
  overwrite_evidence = FALSE,
  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
column_name

(char) The Protein Column Name to map. Options:

  • Leadind razor protein (default)

  • Leading protein

  • Proteins It only supports Uniprot Entry IDs and RefSeq, but it might work for other database IDs
output_file

(char) Output file name (ptmsites-evidence.txt recommended)
mod_type

(char) The posttranslational modification. Options:

  • UB: Protein Ubiquitination

  • PH: Protein Phosphorylation

  • AC: Protein Acetylation

  • PTM:XXX:yy : User defined PTM. Replace XXX with 1 or more 1-letter amino acid codes on which to find modifications (all uppercase). Replace yy with modification name used within the evidence file (require lowercase characters). Example: PTM:STY:ph will find modifications on aa S,T,Y with this format _AAGGAPS(ph)PPPPVR_. This would be equivalent to mod_type = PH
overwrite_evidence

(logical) if <output_file> is the same as <evidence_file>, overwrite_evidence = FALSE (default) doesn't allow to overwrite the evidence file. Otherwise, overwrite_evidence = TRUE allows to overwrite the evidence_file (this option might be activated if the user allows to use the same ptm-sites-evidence.txt file to re-annotate all the Protein IDs columns)
verbose

(logical) TRUE (default) shows function messages

Value

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

Output 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)

#> [1] "Files must not be NULL"