Is there any benefit to using profile (continuum) data over centroided data?
Importing profile (continuum) data into Progenesis means there is more information associated with the file than if you were to import centroided data. This additional information allows Progenesis to accurately filter out background noise from your data during import. The result of this is cleaner runs with more accurate peak detection, quantitation and—ultimately—improved identification of your peptides and proteins. The accurate removal of noise also improves the data compression, so you should get improved software performance too.
You might have some concerns about the space needed on your PC’s hard drive if you’re going to be using profile data but once data has been imported into Progenesis it is compressed and saved as a .mznld file which is much smaller than the original raw data file – you can then archive the raw data, freeing up valuable space on your hard drive but still allowing you to continue with the analysis of the data set.