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Example annotation file for a label-free MaxQuant experiment.

Source: R/dataDoc.R
maxq_lf_annotation.Rd

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)
#>                                     Run Condition BioReplicate
#> 1 20180810_QE3_nLC3_AH_DDA_Yonly_ind_01   H0_Y100   H0_Y100_01
#> 2 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02   H0_Y100   H0_Y100_02
#> 3 20180810_QE3_nLC3_AH_DDA_Yonly_ind_03   H0_Y100   H0_Y100_03
#> 4  20180810_QE3_nLC3_AH_DDA_H100_Y25_01  H100_Y25  H100_Y25_07
#> 5  20180810_QE3_nLC3_AH_DDA_H100_Y25_02  H100_Y25  H100_Y25_08
#> 6  20180810_QE3_nLC3_AH_DDA_H100_Y25_03  H100_Y25  H100_Y25_09
#>                                Raw.file IsotopeLabelType
#> 1 20180810_QE3_nLC3_AH_DDA_Yonly_ind_01                L
#> 2 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02                L
#> 3 20180810_QE3_nLC3_AH_DDA_Yonly_ind_03                L
#> 4  20180810_QE3_nLC3_AH_DDA_H100_Y25_01                L
#> 5  20180810_QE3_nLC3_AH_DDA_H100_Y25_02                L
#> 6  20180810_QE3_nLC3_AH_DDA_H100_Y25_03                L