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.
Details
Run : Run name that matches exactly with MaxQuant 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(maxq_tmt_annotation)
#> Run Fraction TechRepMixture
#> 1 20171106_LUMOS1_nLC13_AH_TechBench2_TMTMS2L_1 1 1
#> 2 20171106_LUMOS1_nLC13_AH_TechBench2_TMTMS2L_1 1 1
#> 3 20171106_LUMOS1_nLC13_AH_TechBench2_TMTMS2L_1 1 1
#> 4 20171106_LUMOS1_nLC13_AH_TechBench2_TMTMS2L_1 1 1
#> 5 20171106_LUMOS1_nLC13_AH_TechBench2_TMTMS2L_1 1 1
#> 6 20171106_LUMOS1_nLC13_AH_TechBench2_TMTMS2L_1 1 1
#> Channel Condition Mixture BioReplicate
#> 1 channel.10 yeast_01x Mixture1 yeast_01x_1
#> 2 channel.1 yeast_04x Mixture1 yeast_04x_1
#> 3 channel.2 yeast_10x Mixture1 yeast_10x_1
#> 4 channel.3 yeast_01x Mixture1 yeast_01x_2
#> 5 channel.4 yeast_04x Mixture1 yeast_04x_2
#> 6 channel.5 yeast_10x Mixture1 yeast_10x_2