fragpipe_annotation: Example annotation file for a TMT FragPipe experiment.

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

Example annotation file for a TMT FragPipe experiment.

Description

Automatically created by FragPipe, manually checked by the user and input into the FragPipetoMSstatsPTMFormat converter. Requires the correct columns and maps the experimental desing into the MSstats format. Specify unique bioreplicates for group comparison designs, and the same bioreplicate for repeated measure designs. The columns and descriptions are below.

Usage

fragpipe_annotation

Format

A data.table with 7 columns.

Details

• Run : Run name that matches exactly with FragPipe run. Used to join evidence and metadata in annotation file.

• Fraction : If multiple fractions were used (i.e. the same mixture split into multiple fractions) enter that here. TechRepMixture : Multiple runs using the same bioreplicate

• Channel : Mixture channel used

• Condition : Name of condition that was used for each run.

• Mixture : The unique mixture (plex) name

• BioReplicate : Name of biological replicate. Repeating the same name here will tell MSstatsPTM that the experiment is a repeated measure design.

Examples

head(fragpipe_annotation)

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