The Reporter Ions Quantifier node performs reporter ion quantification, which uses external reagents, or tags, to enzymatically or chemically label proteins and peptides. The application uses this node in iTRAQ and TMT experiments.

For more information on using the node in a workflow, see Creating Reporter Ion Quantification Workflows.

The following table describes the parameters for the Reporter Ions Quantifier node.

Reporter Ions Quantifier node parameters

Parameter

Definition

Integration Tolerance

Specifies the mass-to-charge window so that you can look for the reporter peaks.

Range: 0.0001–0.6 Da or 0.01–5000 ppm; default: 20 ppm

Integration Method

Specifies which peak to select if more than one peak is found inside the integration window:

  • (Default) Most Confident Centroid: Defines which one of multiple peaks to select. This option lays a Gaussian curve around the target peak (the tag mass) with a sigma value equal to the mass accuracy or integration window. Then the Gaussian curve normalizes all peaks in the window, and the peak that is the largest after that is considered to be the most confident peak.
  • This method is also used by the Spectrum Selector node in the Workflow Editor to pick the monoisotopic peak from the survey scan. The only difference is that the Spectrum Selector node uses a 3-sigma interval, but Most Confident Centroid uses only a 1-sigma interval. This means the Most Confident Centroid is almost always the largest peak inside the integration window because of the small inclination of the Gaussian curve in the 1-sigma interval.
  • Most Intense Centroid: Selects the highest peak.
  • Centroid With Smallest Delta Mass: Selects the peak with the smallest deviation from the theoretical mass.
  • Centroid Sum: Sums the intensity of all the peaks in the window.

Mass Analyzer

Specifies the type of mass spectrometer used in the acquisition of the spectrum:

  • Ion Trap
  • (Default) Fourier Transform
  • Time of Flight
  • Single Quad
  • Triple Quad
  • Sector Field

MS Order

Specifies the level of the mass spectrum to be processed, for example, MS/MS or MS3.

Range: MS2–MS10; default: MS2

Activation Type

Specifies the fragmentation method used for each spectrum:

  • CID (Collision-Induced Dissociation)
  • MPD (Multi-Photon Dissociation)
  • ECD (Electron Capture Dissociation)
  • PQD (Pulsed Q Collision-Induced Dissociation)
  • ETD (Electron Transfer Dissociation)
  • (Default) HCD (High-Energy-Collision Dissociation)
  • EThcD (ETD with Supplemental HCD)
  • UVPD (Ultraviolet Photodissociation)

For descriptions, see Multidimensional separation experiments.

Min. Collision Energy

Filters out fragment spectra with a normalized collision energy below the specified value.

Range: 0–100; default: 0

Max. Collision Energy

Filters out fragment spectra with a normalized collision energy above the specified value.

Range: 0–1000; default: 1000