Pk nextGen

PIKA fitting process steps

 * Preparation for HR fitting

The order of preparatory steps below is generally not modifiable. (1A) Get good m/z calibration parameters. Mike has this code in place for Tofwerk files. (1B) Get good baseline-removed spectra. The purpose of saving copies of the raw spectra with the baseline removed is so that the multipeak fitting is done on the ‘same’ spectra. This insures that the calculation of any baseline isn’t dependent on settings (‘resolution’ interpolations parameters) that could be adjusted by the user and then not saved, not recorded, an hence not replicable. (1C) Get good peak width (PW), peak shape (PS). Getting good values for these parameters is necessarily an iterative process. In general one looks at 100s of sets of isolated HR ions (i.e. C4H9+, etc ) spectra to get good statistics for PW and PS. Once a user is confident that selected HR ions are behaving in a consistent and ‘smooth’ manner, one can set the PW and even PS on an individual run basis if needed. (1D) Select the HR ions to fit. This is highly variable depending on the application. Similar to Mike’s m/z calibration routine, I envision a simple interface whereby a user imports settings appropriate to their type of application. (1E) Select a subset of HR ions in (1D) to be constrained. Constrained means that the fitting routine does not ‘fit’ this HR ion – the peak height is fixed to a value based on the magnitude of the HR ion’s isotopic ‘parent’ that has been previously fit or determined. This has consequences about the order in which UMR sets of HR ions at on m/z are fit.