The proteoQC package is exactly what i was looking for to give me some QC information on proteomic samples, however i am running into two issues. One may be a bug, and the other may be me doing something weird.
The first is that when i am creating the sample list to run with the mQCpipe, it will only work if i have all the headings outlined in the example (file, sample, bioRep, techRep and fraction). I have many biological replicates (currently running 5 biological replicates per 2 samples to test the system but this will typically increase to 10-15 per sample) but i do not run technical replicates or have fractions. To get around this, i have been inserting either 1 or 0 and it has been running fine resulting in a mQC file. Is this a bug in the code, or do i need to specify something indicating that i do not have technical replicates or fractions? I have ran the example sample with this and then removing the fraction and tech and it also does not run which is why i wonder if it is a bug.
Secondly, when i use the reportHTML on my mQC file, the following error appears
Error in names(miss.df) <- c("x", "y") : 'names' attribute  must be the same length as the vector 
Looking into the names, there is an obvious difference where my run returns the following headings ("inputparameter" "resfractionlevel" "restechReplevel" "ressample_level") but does not include the biological replicate column despite this containing most of the sample information.
Any help with this would be much appreciated as i'm running out of ideas.