What are the best default settings for high and low energy intensity threshold counts in the 3D-4D peak processing parameters in UNIFI? - WKB14275

ENVIRONMENT

• UNIFI 1.8.x
• UNIFI 1.9.x

ANSWER

For the "Accurate Mass Screening" analysis method for MSe/HDMSe data, go to processing "Find 3D/4D peak" parameters. The recommended threshold for low energy is 100 counts and for high energy threshold 20 counts. The low energy directly corresponds to the lowest response of peak, which will be retained and shown in the components summary table (either as identified components or as candidate mass) on the Review tab of the analysis.

ADDITIONAL INFORMATION

The thresholds can be further optimized based on data complexity and application to reduce processing time.

With default parameters on Quantify tab of the analysis method:

The detector counts will be the sum of all adducts and isotopes, and the response will be the intensity of the most intense monoisotopic peak. The intensity from the 3D peak volume (or the one observed on the mass spectra) may be converted to response or detector counts with the formula below. The formula normalizes the intensity with the average ion area measured during instrument setup and the mass of the ion.

To convert the ADC Response of a peak (i.e., the sum of voltage pulse areas) into the Detector Counts (i.e., an estimate of the number of ions):

1. Factor = ADCAveIonIntensity * Sqrt(ADCIntenCalMZ / ADCIntenCalZ) * System.Math.Sqrt(IonZ/IonMZ)
2. DetectorCounts = adcResponse / factor

Where:

• ADCAveIonIntensity: the area of the voltage pulse produced by a single reference ion (this is measured during instrument setup)
• ADCIntenCalMZ: the m/z of the reference ion (normally 556.2766)
• ADCIntenCalZ: the charge of the reference ion (normally 1)
• IonMZ: the m/z of the ion we want to estimate the DetectorCounts for
• IonZ: the charge of the ion we want to estimate the DetectorCounts for
• adcReponse: the intensity of the ion (i.e., the sum of the voltage pulses)