ProgenesistoMSstatsPTMFormat {MSstatsPTM} | R Documentation

## Converts non-TMT Progenesis output into the format needed for MSstatsPTM

### Description

Converts non-TMT Progenesis output into the format needed for MSstatsPTM

### Usage

    ProgenesistoMSstatsPTMFormat(
      ptm_input,
      annotation,
      global_protein_input = FALSE,
      fasta_path = FALSE,
      useUniquePeptide = TRUE,
      summaryforMultipleRows = max,
      removeFewMeasurements = TRUE,
      removeOxidationMpeptides = FALSE,
      removeProtein_with1Peptide = FALSE,
      mod.num = "Single"
    )

### Arguments

`ptm_input` | name of Progenesis output with modified peptides, which is wide-format. 'Accession', Sequence', 'Modification', 'Charge' and one column for each run are required
`annotation` | name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run, and Type (PTM or Protein) information. It will be matched with the column name of input for MS runs. Please note PTM and global Protein run names are often different, which is why an additional Type column indicating Protein or PTM is required.
`global_protein_input` | name of Progenesis output with unmodified peptides, which is wide-format. 'Accession', Sequence', 'Modification', 'Charge' and one column for each run are required
`fasta_path` | string containing path to the corresponding fasta file for the modified peptide dataset.
`useUniquePeptide` | TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
`summaryforMultipleRows` | max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
`removeFewMeasurements` | TRUE (default) will remove the features that have 1 or 2 measurements across runs.
`removeOxidationMpeptides` | TRUE will remove the modified peptides including 'Oxidation (M)' sequence. FALSE is default.
`removeProtein_with1Peptide` | TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
`mod.num` | For modified peptide dataset, must be one of `Single` or `Total`. The default is `Single`. The number modifications per peptide to be used. If "Single", only peptides with one modification will be used. Otherwise "Total" includes peptides with more than one modification. Selecting "Total" may confound the effect of different modifications.

### Value

a list of two data.tables named 'PTM' and 'PROTEIN' in the format required by MSstatsPTM.

### Examples

    # Example annotation file
    annotation <- data.frame('Condition' = c('Control', 'Control', 'Control',
                             'Treatment', 'Treatment', 'Treatment'),
                             'BioReplicate' = c(1,2,3,4,5,6),
                             'Run' = c('prot_run_1', 'prot_run_2', 'prot_run_3',
                                      'phos_run_1', 'phos_run_2', 'phos_run_3'),
                             'Type' = c("Protein", "Protein", "Protein", "PTM",
                                        "PTM", "PTM"))

    # The output should be in the following format.
    head(raw.input$PTM)
    head(raw.input$PROTEIN)

[Package MSstatsPTM version 1.2.4 Index]