I have some Waters raw files in profile mode and I can't convert them to centroid. I already tried to use the proteowizard and, unfortunately, it continues as a profile.

Does anyone know another way to perform this conversion from profile to centroid?

Thank you.

Hi - this isn't a Bioconductor question, but I can provide a Bioconductor answer.

• The MSnbase and Spectra packages (the latter being the successor of the former) have a pickPeaks() function that pick peaks in profile mode data to generate centroided data. You will however need to check that this generates adequate results for your data.
• I am very surprised that proteowizard's msconvert wasn't able produce centroided data - you might need to check the command you used and/or ask for help on the proteowizard mailing list.