MassQC Help > Metrics > MS1 > Peak Intensity          
MS1 Peak Intensity

Peak intensity is the intensity at the highest point of the MS1 peak for a peptide.

Higher Peak Intensities mean that the mass spectrometer is registering higher readings for the peptides, that is, increased sensitivity.

The Peak Intensity metric is the median of the MS1 peak intensities. This metric only considers MS1 peaks that have an MS2 spectrum that has been matched to a peptide. It also only considers MS1 peaks that elute during the "Retention Spread", the elution time span where most of the peptides are eluting.


Log (base 10) of intensity units defined by the mass spectrometer


Higher: More intense peaks are easier to detect.

What the Metric Detects:

The Peak Intensity measures how much signal is available for detecting peptides. This measure is sensitive to the amount of sample loading into the LC-MS system.

Related Metrics:

The Peak Intensity is the amount of ion current that is associated with peptides. The Total Ion Current includes the ion current from all ions. That is not only ions for identified peptides and but also ions that are from any other source (contaminants, noise, unidentified peptides, etc.) If the Total Ion Current increases but the Peak Intensity does not, this may indicate an increase in contaminates.

The Dynamic Range estimates the range between the more intense peaks and lowest intensity peaks that are still detected. Together the Peak Intensity and Dynamic Range give the median and range of the distribution of peptide peak intensities.

The Trigger Point tells where on the MS1 peak the MS2 is triggered. If MS2 is triggered at a set level, higher Peak Intensities may mean that the Trigger Point will be a lower percentage of the peak maximum.

The Low Intensity Trigger Point and Low Intensity ID Rate are measured only when the Peak Intensity is low.

Related Troubleshooting Topics:

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