MassQC Help > Metrics > Identifications > Peptide Count          
Peptide Count

Peptide Count is the number of unique peptides.

Higher numbers of unique identified tryptic peptides indicate generally improved instrument performance, making Peptide Count a good overall measure.

The Peptide Count metric is the number of unique tryptic peptide sequences identified. Modified versions of the peptide do not add to the Peptide Count. Also ignored in this count are multiple spectra matching the peptide and ions with different charge states.

Peptide Count




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:

The Peptide Count metric measures the overall effectiveness of the LC-MS system for identifying peptides. Since it measures the overall health of the instrument, Peptide Count is not particularly useful for diagnosing problems with particular components of the LC-MS system.

Related Metrics:

Peptides per Minute tells how fast the peptides are being detected during the time when they are eluting the fastest (Retention Spread).

The High Intensity ID Rate and Low Intensity ID Rate tell what percent of the MS2 spectra are being identified for intense and weak peaks respectively.

Related Troubleshooting Topics:

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