Example of input PTM dataset for LabelFree/DDA/DIA experiments.

Source: R/dataDoc.R

It can be the output of MSstatsPTM converter ProgenesistoMSstatsPTMFormat or other MSstats converter functions (Please see MSstatsPTM_LabelFree_Workflow vignette). The dataset is formatted as a list with two data.tables named PTM and PROTEIN. In each data.table the variables are as follows:

raw.input

Format

A list of two data.tables named PTM and PROTEIN with 1745 and 478 rows respectively.

Details

  • ProteinName : Name of protein with modification site mapped in with an underscore. ie "Protein_4_Y474"

  • PeptideSequence

  • Condition : Condition (ex. Healthy, Cancer, Time0)

  • BioReplicate : Unique ID for biological subject.

  • Run : MS run ID.

  • Intensity

  • PrecursorCharge

  • FragmentIon

  • ProductCharge

  • IsotopeLabelType

Examples

head(raw.input$PTM)

#> # A tibble: 6 x 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.
#> # ... with 4 more variables: PrecursorCharge <chr>, FragmentIon <lgl>,
#> #   ProductCharge <lgl>, IsotopeLabelType <chr>
head(raw.input$PROTEIN)

#> # A tibble: 6 x 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.
#> # ... with 4 more variables: PrecursorCharge <chr>, FragmentIon <lgl>,
#> #   ProductCharge <lgl>, IsotopeLabelType <chr>