I have set of 6,files 3 control and 3 test replicates.

I did see bioconductor packages like msnbase where i can see how the files are read etc. But so far im not able find or search proper resource which can give me idea about from input file which are in mzxml format to the peak annotation

My objectives are

1. Centroiding of profile MS data using peak picking
2. Improving the signal quality with data smoothing and refinement of the centroids m/z values
3. Followed by peak detection using CentWave method
4. Final is the metabolite identification

Any resources which shows can give idea about doing these would be really helpful .