MassQC Help > Metrics > MS2 > Signal to Noise          
MS2 Signal to Noise

Signal to Noise estimates how strong the signal is, that is how much larger the large peaks in the spectrum compared to the the background noise.

Signal to Noise indicates the strength of the signal that can be used to identify peptides.

The MS2 Signal to Noise metric is estimated by taking the ratio of the maximum to the median of the fragment ion peak heights. The Signal to Noise metric is calculated for the MS2 spectra that are matched to a peptide. Signal to Noise looks only at peak heights: it does not taking into account which peaks are the b or y fragment ions.

Units:

Ratio of Signal to Noise

Optimal:

Higher

The most reproducible LC-MS performance is when this metric remains in a narrow range over a series of runs. Wide variability in any metric means your process is not reproducible.

What the Metric Detects:

MS2 Signal to Noise estimates the signal strength.

Related Metrics:

The good MS2 Signal to Noise and a fair number of Peaks per Spectrum will usually correlate with a spectrum that is easy for the search engines to match to a peptide. This is expected to correlate with a high Search Score. If it doesn't, that may mean that the peptides in the sample are contaminants for which the search engine isn't looking.

Related Troubleshooting Topics:
Forum:

If you have questions, comments and/or insights about MassQC, you can share them on the MassQC Users Forum.

Search the MassQC Site and the Help Center: