Extract information from MaxQuant logs

Read MaxQuant (mqpar.xml) file and extract information about the run.

readMaxQuantXML(mqParameterFile)

Arguments

mqParameterFile

Character scalar, the path to a MaxQuant parameter file. Can be NULL (in this case, an empty list is returned).

Value

A list with extracted information about the MaxQuant run.

Author

Charlotte Soneson

Examples

readMaxQuantXML(system.file("extdata", "mq_example",
                            "1356_mqpar.xml",
                            package = "einprot"))
#> $`MaxQuant version`
#> [1] "1.5.3.8"
#> 
#> $`Parameter file`
#> [1] "/Users/runner/work/_temp/Library/einprot/extdata/mq_example/1356_mqpar.xml"
#> 
#> $`Search engine`
#> [1] "Andromeda"
#> 
#> $`Raw file location`
#> [1] "D:/Data/MaxQuant/"
#> 
#> $`Raw files`
#> [1] "F_160817_AdnpFB_IP04.raw, F_160817_AdnpFB_IP05.raw, F_160817_AdnpFB_IP06.raw, F_160817_Chd4BF_IP07.raw, F_160817_Chd4BF_IP08.raw, F_160817_Chd4BF_IP09.raw, F_160817_RBC_ctrl_IP01.raw, F_160817_RBC_ctrl_IP02.raw, F_160817_RBC_ctrl_IP03.raw"
#> 
#> $`Sample names`
#> [1] "Adnp_IP04, Adnp_IP05, Adnp_IP06, Chd4BF_IP07, Chd4BF_IP08, Chd4BF_IP09, RBC_ctrl_IP01, RBC_ctrl_IP02, RBC_ctrl_IP03"
#> 
#> $Databases
#> [1] "D:/Databases/MOUSE__150129.fasta"
#> 
#> $Contaminants
#> [1] "*/MaxQuant_1.5.3.8/MaxQuant/bin/conf/contaminants.fasta"
#> 
#> $`Quantification settings (LFQ)`
#> [1] "LFQ min. ratio count: 1, fastLFQ: false, match-between runs (MBR): true, Intensity based absolute quantification (iBAQ): true"
#> 
#> $`Min. razor peptides`
#> [1] "1"
#> 
#> $Enzymes
#> [1] "Trypsin/P"
#> 
#> $`Variable modifications`
#> [1] "Oxidation (M), Acetyl (Protein N-term)"
#> 
#> $`Fixed modifications`
#> [1] ""
#> 
#> $`Max peptide mass`
#> [1] "8000"
#> 
#> $`Min peptide length`
#> [1] "7"
#>