I am looking to convert data from my LC-MS (Waters G2 Synapt) to netCDF in order to import into another platform. Unfortunately netCDF is the only import option available. Waters Masslynx contains a netCDF export tool, however it is hard wired to centroid the data first and I need non-centroided data (profile/continuum).
I can convert to a suitable import format (mzXML for example) using ProteoWizard but then need to convert to netCDF. One of the PWiz devs suggested that XCMS can do it but I cannot see this explicitly stated in the package literature.
MAIN QUESTION - If I supply non-centroided data to XCMS, can it translate it to netCDF without performing any processing (centroiding, peak picking).
BONUS QUESTION - I will float this to the ethers, but does anyone know of a better tool to get from Waters.raw to netCDF?
BONUS QUESTION 2 - Is there a Bioconductor app in development that could take the output from XCMS (peak picking), identify ESI-MS protein charge state profiles and deconvolute the mass? The problem I am having is the identification of protein charge state envelopes from a complex LC-ESI-MS run containing dozens or more protein species without relying on chromatographic integration (many proteins are invisible in a BPI trace, too many co-elutions in a TIC chromatogram and there are abundant proteins under flat baseline in TIC chromatograms.
The main question is what I really need answered, the other two are bonus.
Thanks in advance,