Quantification

Sage can perform fast and accurate label-free and isobaric (i.e. TMT) quantification. The following settings can be used to configure quantification:

{
 "quant": {
    "tmt": "Tmt16",
    "tmt_settings": {
      "level": 3,
      "sn": false
    },
    "lfq": true,
    "lfq_settings": {
      "peak_scoring": "Hybrid",
      "integration": "Sum",
      "spectral_angle": 0.7,
      "ppm_tolerance": 5.0
    }
  }
}

TMT

• tmt: String. One of "Tmt6", "Tmt10", "Tmt11", "Tmt16", or "Tmt18" (default: null).
• tmt_settings: Object containing TMT-specific settings.
  • level: Integer. The MS-level to perform TMT quantification on (default: 3).
  • sn: Boolean. Use Signal/Noise instead of intensity for TMT quantification. Requires noise values in mzML (default: false).

If you need to report S/N measurements, ThermoRawFileParser (opens in a new tab) supports adding noise values to mzMLs.

LFQ

• lfq: Boolean. Perform label-free quantification (default: null).
• lfq_settings: Object containing LFQ-specific settings.

  • peak_scoring: String. The method used for scoring peaks in LFQ, one of: "Hybrid", "RetentionTime", "SpectralAngle" (default: "Hybrid").

    Hybrid scoring combines RT-based and spectral-angle based scoring to identify the best MS1 peak to quantify.

  • integration: String. The method used for integrating peak intensities, either "Sum" or "Max" (default: "Sum").

  • spectral_angle: Float. Threshold for the normalized spectral angle similarity measure (observed vs theoretical isotopic envelope), ranging from 0 to 1 (default: 0.7).

  • ppm_tolerance: Float. Tolerance for matching MS1 ions in parts per million (default: 5.0).