Skip to contents

Convert Peaks Studio output into MSstatsPTM format

Source: R/converters.R
PStoMSstatsPTMFormat.Rd

Currently only supports label-free quantification.

Usage

PStoMSstatsPTMFormat(
  input,
  annotation,
  input_protein = NULL,
  annotation_protein = NULL,
  use_unmod_peptides = FALSE,
  target_modification = NULL,
  remove_oxidation_peptides = FALSE,
  remove_multi_mod_types = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

input

name of Peaks Studio PTM output

annotation

name of annotation file which includes Raw.file, Condition, BioReplicate, Run. For example annotation see example below.

input_protein

name of Peaks Studio unmodified protein output (optional)

annotation_protein

name of annotation file which includes Raw.file, Condition, BioReplicate, Run for unmodified protein output.

use_unmod_peptides

Boolean if the unmodified peptides in the input file should be used to construct the unmodified protein output. Only used if input_protein is not provided. Default is FALSE

target_modification

Character name of modification of interest. To use all mod types, leave as NULL. Default is NULL. Note that if the name includes special characters, you must include "\" before the characters. Ex. "Phosphorylation \(STY\)"

remove_oxidation_peptides

Boolean if Oxidation (M) modifications should be removed. Default is FALSE

remove_multi_mod_types

Used if target_modification is not NULL. TRUE will remove peptides with multiple types of modifications (ie acetylation and phosphorylation). FALSE will keep these peptides and summarize them seperately.

summaryforMultipleRows

max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.

use_log_file

logical. If TRUE, information about data processing will be saved to a file.

append

logical. If TRUE, information about data processing will be added to an existing log file.

verbose

logical. If TRUE, information about data processing wil be printed to the console.

log_file_path

character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file.

Value

list of data.table

Examples

# The output should be in the following format.
head(raw.input$PTM)
#> # A tibble: 6 × 10
#>   ProteinName PeptideSequence Condition BioReplicate Run        Intensity
#>   <chr>       <chr>           <chr>     <chr>        <chr>          <dbl>
#> 1 Q9UHD8_K262 DAGLK*QAPASR    CCCP      BCH1         CCCP-B1T1   1423906.
#> 2 Q9UHD8_K262 DAGLK*QAPASR    CCCP      BCH1         CCCP-B1T2    877045.
#> 3 Q9UHD8_K262 DAGLK*QAPASR    CCCP      BCH2         CCCP-B2T1    384418.
#> 4 Q9UHD8_K262 DAGLK*QAPASR    CCCP      BCH2         CCCP-B2T2    454858.
#> 5 Q9UHD8_K262 DAGLK*QAPASR    Combo     BCH1         Combo-B1T1  1603377.
#> 6 Q9UHD8_K262 DAGLK*QAPASR    Combo     BCH1         Combo-B1T2   676555.
#> # ℹ 4 more variables: PrecursorCharge <chr>, FragmentIon <lgl>,
#> #   ProductCharge <lgl>, IsotopeLabelType <chr>
head(raw.input$PROTEIN)
#> # A tibble: 6 × 10
#>   ProteinName PeptideSequence Condition BioReplicate Run           Intensity
#>   <chr>       <chr>           <chr>     <chr>        <chr>             <dbl>
#> 1 Q9UHD8      STLINTLFK       CCCP      BCH2         CCCP-B2T1       367944.
#> 2 Q9UHD8      STLINTLFK       CCCP      BCH2         CCCP-B2T2       341207.
#> 3 Q9UHD8      STLINTLFK       Combo     BCH2         Combo-B2T1      185843.
#> 4 Q9UHD8      STLINTLFK       Ctrl      BCH2         Ctrl-B2T1       529224.
#> 5 Q9UHD8      STLINTLFK       Ctrl      BCH2         Ctrl-B2T2       483355.
#> 6 Q9UHD8      STLINTLFK       USP30_OE  BCH2         USP30_OE-B2T1   447795.
#> # ℹ 4 more variables: PrecursorCharge <chr>, FragmentIon <lgl>,
#> #   ProductCharge <lgl>, IsotopeLabelType <chr>