artmsProtein2SiteConversion {artMS} | R Documentation |
Proteins
column of the evidence file to site-specific
Uniprot_PTM
notationIt 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:
Uses p
instead of (ph)
The modified residue (i.e. STY) is the residue on the left of the p
,
instead of the residue to the right of (ph)
as usual.
These changes significantly affect the algorithm used by this artMS function
to extract the PTM site information. We are working on debugging the issue
and use an alternative function independent of the "Mofified sequence"
column. If your MaxQuant version is affected, then the column mod_sites
of
the output -mapping.txt
will have many NA values for peptides with p
modifications (and no NA values should be present)
artmsProtein2SiteConversion(evidence_file, ref_proteome_file, output_file, mod_type, verbose = TRUE)
evidence_file |
(char) The evidence file name and location |
ref_proteome_file |
(char) The reference proteome used as database
to search the |
output_file |
(char) Output file name
( |
mod_type |
(char) The posttranslational modification. Options:
|
verbose |
(logical) |
(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
.
# Testing warning if files are not submitted artmsProtein2SiteConversion(evidence_file = NULL, ref_proteome_file = NULL, output_file = NULL)