summary.data.tmt {MSstatsPTM} | R Documentation

## Example of output from dataSummarizationPTM_TMT function for TMT data

### Description

It is made from `raw.input.tmt`. It is the output of dataSummarizationPTM_TMT function from MSstatsPTM. It should include a list with two names `PTM` and `PROTEIN`. Each of these list values is also a list with two names `ProteinLevelData` and `FeatureLevelData`, which correspond to two data.tables.The columns in these two data.tables are listed below. The variables are as follows:

- FeatureLevelData :

  - ProteinName : MS run ID

  - PSM : Protein ID with modification site mapped in. Ex. Protein_1002_S836

  - censored: Protein-level summarized abundance

  - predicted : Labeling information (126, ... 131)

  - log2Intensity : Condition (ex. Healthy, Cancer, Time0)

  - Run : Unique ID for biological subject.

  - Channel : Unique ID for technical replicate of one TMT mixture.

  - BioReplicate : Unique ID for TMT mixture.

  - Condition : Unique ID for TMT mixture.

  - Mixture : Unique ID for TMT mixture.

  - TechRepMixture : Unique ID for TMT mixture.

  - PeptideSequence : Unique ID for TMT mixture.

  - Charge : Unique ID for TMT mixture.

- ProteinLevelData :

  - Mixture : MS run ID

  - TechRepMixture : Protein ID with modification site mapped in. Ex. Protein_1002_S836

  - Run: Protein-level summarized abundance

  - Channel : Labeling information (126, ... 131)

  - Protein : Condition (ex. Healthy, Cancer, Time0)

  - Abundance : Unique ID for biological subject.

  - BioReplicate : Unique ID for technical replicate of one TMT mixture.

  - Condition : Unique ID for TMT mixture.

### Usage

    summary.data.tmt

### Format

A list of two lists with four data.tables.

### Examples

    head(summary.data.tmt)

[Package MSstatsPTM version 1.2.4 Index]