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.

Table ProSightPD Med/High cRAWler Node parameters

Parameter

Description

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:

  • Standard—Groups MS/MS scans within retention time and m/z tolerances and groups the corresponding MS scans.
  • PTCR—Groups a single fragmentation scan with its corresponding PTCR precursor scan.

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:

  • Never—Always uses algorithm detected masses (Default)
  • Always—Uses only the manually input Precursor Mass parameter for every target mass
  • If not detected—When the Xtract algorithm does not detect a mass, the manually input Precursor Mass parameter is used for the target

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:

  • High—All available threads less 1
  • Medium—50% of the available threads
  • Low—1 thread

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.