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.

Table ProSightPD PTCR 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

The maximum difference in precursor isolation m/z allowed for grouping of subsequent MS/MS scans.

Grouper

Defines 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 APD Parameters

Use Manual Precursor Mass

Selects from the following:

  • Never: Always uses APD detected masses
  • Always: Only uses the manually input Precursor Mass parameter for every target mass
  • If not detected: When no mass is detected by APD 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

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:

  • High—All available threads less 1 (Default)
  • 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

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.