raw.protein: Example of input Protein dataset for TMT experiments.

In Vitek-Lab/MSstatsTMTPTM: Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Description

It can be the output of PDtoMSstatsTMTFormat or other MSstatsTMT converter functions. It includes peak intensities for a variety of PTMs. This is the companion file to the raw.ptm dataset, includes unmodified protein data. The variables are as follows:

Usage

raw.protein

Format

A data frame with 620476 rows and 11 variables.

Details

• ProteinName : Name of protein

• 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.protein)

Vitek-Lab/MSstatsTMTPTM documentation built on Oct. 25, 2021, 10:55 a.m.