Percent +4H is the percentage of all spectra matching peptides that have a charge of +4.
Higher Percent +4H indicates that the mass spectrometer may favor long peptides.
Percent +4H is calculated by looking at the charge state of all spectra that match to a peptide.
Percent (%)
Consistent
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.
A high Percent +4H means that there are an unusual number of plus 4 ions. This might mean that the electrospray is behaving erratically..
Large Percent +4H means that the other charge states don't get as many ions. The metrics Percent +1H and Percent +3H also report the ion's charge state. Any ions that are not charge +1, +3, or +4 are probably charge +2.
If the distribution of charge differs, it may affect the size of the peptides that are detected. Another way to look at this is with the metric Precursor m/z.
If you have questions, comments and/or insights about MassQC, you can share them on the MassQC Users Forum.