maxq_lf_annotation: Example annotation file for a label-free MaxQuant experiment.

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

Example annotation file for a label-free MaxQuant experiment.

Description

Must be manually created by the user and input into the MaxQtoMSstatsPTMFormat 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

maxq_lf_annotation

Format

A data.table with 5 columns.

Details

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

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

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

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

• IsotopeLabelType: Name of isotope label. May be all L or unique depending on experimental design.

Examples

head(maxq_lf_annotation)

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