I'm using MS/MS for label-free quantification in metaproteomics. I've run the database searching (MSGF+) with mzML files, and the output is .mzid files. Then, I've used the MSnID and mzid R packages to calculate/optimize False Discovery Rate cutoffs, and applied these cutoffs. I'm confused about where MSnbase (Gatto and Lilley, 2012; Bioinformatics) comes into play here. I know that there are a large amount of tools available for analyzing and processing MS data in MSnbase.
So, what is the recommended workflow for quantification and applying an optimized FDR? In the MSnbase documentation (which is great!), it uses an mzML input file for the 'quantify()' function (under 'Label Free MS2 Quantitation/Peptide Counting'). So does this mzML not have an optimized FDR applied to it? Any advice for the next steps of quantification is greatly appreciated! Thanks!