The PTCR cRAWler node processes PTCR precursor data with the APD algorithm and uses the Xtract algorithm to deconvolute fragmentation spectra.
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 | The maximum difference in precursor isolation m/z allowed for grouping of subsequent MS/MS scans. |
Grouper | Defines the grouping method:
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2. Precursor APD Parameters | |
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 | Allows the instrument to determine the precursor mass. |
Apply Precursor Spectral Shift | The decision whether or not to shift the spectrum by a ppm (part per million) shift. |
Precursor Spectral Shift | The ppm amount to shift the spectrum. Minimum value: -100 Maximum value: 100 |
3. Fragmentation Xtract Parameters | |
S/N Threshold | The minimum signal to noise threshold for a peak that the Xtract algorithm processes. |
Lowest m/z | The lowest m/z considered by the Xtract algorithm. |
Highest m/z | The highest m/z considered by the Xtract algorithm. |
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. |
Apply Fragment Spectral Shift | The decision whether or not to shift the spectrum by a ppm (part per million) shift. |
Fragment Spectral Shift (ppm) | The ppm amount to shift the spectrum. Minimum value: -100 Maximum value: 100 |
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 | Only consider additional precursors greater than the set value. |
Absolute Minimum Fragment Intensity | Only considered 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. |