To implement the second criteria, we assume that a tolerance value (epsilon > 0) is given by the planners.
Therefore, a tolerance value of 5 (0.5 × 10) was chosen as the candidate tolerance value for FPC contig assembly, with all fragment sizes of each fingerprint multiplied by 10 [ 38].
It was also carried out by using a mass tolerance value of 2 Da for precursor ion and 0.8 Da for MS/MS fragments, trypsin as proteolytic enzyme, and a missed cleavages maximum value of 2. Candidates with >2 assigned peptides with an individual MASCOT score >25, both corresponding to P<0.05 for a significant identification, were considered as confidently identified.
Data were searched by using a mass tolerance value of 2 Da for precursor ion and 0.8 Da for MS/MS fragments, trypsin as proteolytic enzyme, a missed cleavages maximum value of 2 and Cys carbamidomethylation and Met oxidation as fixed and variable modification, respectively.
Therefore it is reasonable (i) to adjust the relative sizes μ m /2 m of the RSA pattern classes by choosing an appropriate tolerance value (τ = 0, 1 or 2) and (ii) to normalize the absolute frequency by dividing by the respective relative pattern class size.
Third, multicollinearity and singularity were tested by calculating tolerance value and variance inflation factor (VIF).
In particular, MALDI-TOF PMF data were searched using a mass tolerance value of 40 80 ppm; nanoLC-ESI-LIT-MS/MS data were searched by using a mass tolerance value of 2 Da for precursor ion and 0.8 Da for MS/MS fragments.
The test is considered a pass if the timing of Start is near the timing of Cln3 peak by the specified tolerance value.
Moreover, multicollinearity of the variables was checked by examining the Tolerance value (the reciprocal of the Tolerance value is the Variance Inflation Factor, VIF), which was ≥ 0.60 [ 57] and, consequently, financial satisfaction was excluded from the multivariate analyses.
