Skip to contents

Example annotation file for a label-free Proteome Discoverer experiment.

Source: R/dataDoc.R
pd_annotation.Rd

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

pd_annotation

Format

A data.table with 3 columns.

Details

  • Run : Run name that matches exactly with PD 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.

Examples

head(pd_annotation)
#>                                         Run Condition BioReplicate
#> 1 20180810_QE3_nLC3_AH_DDA_Yonly_ind_01.raw   H0_Y100   H0_Y100_01
#> 2 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02.raw   H0_Y100   H0_Y100_02
#> 3 20180810_QE3_nLC3_AH_DDA_Yonly_ind_03.raw   H0_Y100   H0_Y100_03
#> 4 20180810_QE3_nLC3_AH_DDA_Honly_ind_01.raw   H100_Y0   H100_Y0_04
#> 5 20180810_QE3_nLC3_AH_DDA_Honly_ind_02.raw   H100_Y0   H100_Y0_05
#> 6 20180810_QE3_nLC3_AH_DDA_Honly_ind_03.raw   H100_Y0   H100_Y0_06