raw.input.tmt: Example of input PTM dataset for TMT experiments.

raw.input.tmtR Documentation

Example of input PTM dataset for TMT experiments.

Description

It can be the output of MSstatsPTM converter MaxQtoMSstatsPTMFormat or other MSstatsTMT converter functions (Please see MSstatsPTM_TMT_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:

Usage

raw.input.tmt

Format

A list of two data.tables named PTM and PROTEIN with 1716 and 29221 rows respectively.

Details

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

  • PeptideSequence

  • Charge

  • PSM

  • Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in a single mass spectrometry experiment. If the channal doesn't have sample, please add ⁠Empty' under Condition. \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates. For example, if ⁠TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match with same ⁠Mixture' value. \item Run : MS run ID. \item Channel : Labeling information (126, ... 131). \item Condition : Condition (ex. Healthy, Cancer, Time0) \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add ⁠Empty' under BioReplicate.

  • Intensity

Examples

head(raw.input.tmt$PTM)
head(raw.input.tmt$PROTEIN)


Vitek-Lab/MSstatsPTM documentation built on Sept. 26, 2024, 9:28 p.m.