The Med/High cRAWler node provides mass assignments for precursor species in medium-high data with unresolved isotope distributions. The Med/High cRAWler node uses an iterative charge-state assignment approach to examine the most abundant m/z species in a spectrum and find real charge-state distributions. This approach is suitable for mass determination of larger mass precursor species.
The following table lists the node parameters.
Parameter | Description |
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1. Chromatographic Parameters | |
Max. RT Difference[min] | The maximum time elapsed between MS/MS scans to be grouped together into a target. |
Precursor m/z Tolerance | Specifies the maximum difference in precursor isolation m/z allowed for grouping of subsequent MS/MS scans. |
Grouper | The grouping method:
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2. Precursor kDecon Parameters | |
Max Precursor Mass | Specifies the maximum precursor mass to consider. |
Min Precursor Mass | Specifies the minimum precursor mass to consider. |
Number Of Results | The maximum number of mass results to return for each averaged scan. The node filters the results by S/N before returning them. |
Number of Iterations | The number of times to run the node. After each iteration, the node removes charge-state distributions from each mass contained in the spectrum to limit false positives during subsequent iterations. |
S/N Result Cutoff | The geometric mean signal to noise ratio (S/N) is calculated from the individual S/N of each charge state in the charge state distribution of a detected mass. |
Full Noise Reduction | Specifies whether to use a QuickHull algorithm to reduce noise. When set to False, the node removes peaks that are not above an exponential moving average. |
Use Manual Precursor Mass | Selects from the following:
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Precursor Mass (Da) Override | User-defined precursor mass in Daltons. |
Use Instrument Determined Precursor Mass | Sets precursor mass determined by the instrument. |
Charge State Intensity Type | The intensity returned for each mass is the sum of the detected charge states. If this parameter is set to Charge Normalized, the intensity of each charge state is divided by its charge. |
Sum Centroid Intensities | If set to True, all intensity values that are part of the centroided peak are summed together. If set to False, only the most abundant m/z value is used. |
3. Fragmentation Xtract Parameters | |
S/N Threshold | The minimum S/N value for processing a peak. |
Lowest m/z | Lowest m/z value to consider. |
Highest m/z | Highest m/z value to consider. |
Lowest Charge | The lowest charge considered by the Xtract algorithm. |
Highest Charge | The highest charge considered by the Xtract algorithm. |
Fit Factor | The minimum pattern accuracy for an isotopic distribution to be considered a valid Xtract mass. |
Overlapping Remainder | Minimum relative remaining intensity of an isotope pattern overlapped by another pattern to be considered. |
Resolution at m/z 400 | Instrumental Resolution at m/z 400 |
4. Multithreading Options | |
CPU Usage | Determines the amount of CPU to direct toward processing:
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5. Data Reduction Parameters | |
Enable Noise Reduction | Makes the following noise reduction parameters available. |
Relative Multiple Precursor Threshold | Consider only additional precursors greater than the set value. |
Absolute Minimum Fragment Intensity | Consider only fragments with intensity greater than the set value. |
Window Size Below | Bin size below m/z 2000 for considering fragments. |
Window Size Above | Bin size above m/z 2000 for considering fragments. |
Fragments per window size above | Number of fragments per bin above m/z 2000 to consider. |
Fragments per window size below | Number of fragments per bin below m/z 2000 to consider. |
Minimum Fragment Count | Minimum number of fragments for a target to be searched. |
Number of Precursors Per Experiment | Maximum number of precursors for a given experiment. |
6. Misc. | |
Heavy Labeled | Heavy isotope labeling can be applied here. None: Standard C13: All carbons are C13. N15: All nitrogens are N15. C13 & N15: All carbons are C13 and all nitrogens are N15. |