For some data (such as Thermo Orbitrap data), the MS/MS spectra may have a precursor mass prediction already. The Kojak algorithm can be set to either ignore, use, or supplement this information using this parameter. There are three options for the parameter:
0 = Ignore all precursor mass predictions and have Kojak make new predictions using its precursor processing algorithms. 1 = Use the existing precursor mass predictions and skip further processing with Kojak. 2 = Use the existing precursor mass predictions and supplement these values with additional results of the Kojak precursor processing algorithms.
The recommended value to use is 2. Supplementing the precursor values performs the following functions. First, the monoisotopic precursor mass may be refined to one determined from a point near the apex of the extracted ion chromatogram, with potentially better mass accuracy. Second, in cases where the monoisotopic peak mass might not have been predicted correctly in the original analysis, a second monoisotopic mass is appended to the spectrum, allowing database searching to proceed checking both possibilities. Third, in cases where there is obvious chimeric signal overlap, a spectrum will be supplemented with the potential monoisotopic peak masses of all presumed precursor ions.
Regardless of this parameter setting, MS/MS spectra that do not have an existing precursor mass prediction will be analyzed to identify the monoisotopic precursor mass using functions built into Kojak.
prefer_precursor_pred = 1