Table 2 Main processing parameters and values used in analysis
Category | Parameter | Function | ShewFed028_LTQFT_1_29May05_Andro_0505-02 | Caulo_084_run3_03Nov06_Andro_06-06-12 | EIF_NAF_CF_Cys1_21Oct06_OWL_06-08-02 |
|---|---|---|---|---|---|
Peak Picking | Peak-Fit Type | Sets the type of peak-fitting to be performed (APEX, LORENTZIAN or Quadratic) | Quadratic | Quadratic | Quadratic |
| Â | S/N | Sets the signal-noise ratio as the ratio of maximum peak intensity to the minimum of floor intensities on either side of the peak | 3 | 3 | 3 |
| Â | Minimum Background Ratio | Sets the maximum intensity level to be considered as background | 3 | 3 | 3 |
Horn Transform Parameters | Charge mass | Mass of charge carrier | 1.007276 | 1.007276 | 1.007276 |
| Â | Max mass | Maximum mass to consider | 10000 | 10000 | 10000 |
| Â | Max charge | Maximum charge to consider | 10 | 10 | 10 |
| Â | Set_THRASH | If set, scores each isotopic profile in stops of +/- 1 Da for fit to data, exits and returns if new_score > current_score | True | True | True |
| Â | Set_Complete_Fit | If set, works same as THRASH except the best fit from a series of fits is returned | False | False | False |
| Â | Distribution-Fit Type | Sets the method of fitting theoretical and observed distributions (Area, Peak or Chi-Squared) | Area | Area | Area |
| Â | Allowable shoulders | Sets the number of allowable shoulders as the number of non-decreasing peaks preceding a minima for it to be considered a shoulder | 1 | 1 | 1 |
| Â | Max_Fit | Range 0 to 1, measure the maximum difference allowable between theoretical and observed distribution | 0.15 | 0.25 | 0.15 |
| Â | Threshold intensity for score | Sets the minimum normalized intensity (0-100) for selection of the area of the peak that will be used for fit calculation | 10 | 10 | 10 |
|  | Threshold intensity for deletion | Sets the intensity threshold (normalized 0 – 100) that determines which areas of a peak are to be deleted. | 1 | 1 | 1 |