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

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

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.