posted on 2021-07-15, 18:07authored byXiaoyu Yang, Pedatsur Neta, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Concepcion A. Remoroza, Meghan C. Burke, Yuxue Liang, Sanford P. Markey, Stephen E. Stein
Annotating
product ion peaks in tandem mass spectra is essential
for evaluating spectral quality and validating peptide identification.
This task is more complex for glycopeptides and is crucial for the
confident determination of glycosylation sites in glycoproteins. MS_Piano
(Mass Spectrum Peptide Annotation) software was developed for reliable
annotation of peaks in collision induced dissociation (CID) tandem
mass spectra of peptides or N-glycopeptides for given peptide sequences,
charge states, and optional modifications. The program annotates each
peak in high or low resolution spectra with possible product ion(s)
and the mass difference between the measured and theoretical m/z values. Spectral quality is measured
by two major parameters: the ratio between the sum of unannotated
vs all peak intensities in the top 20 peaks, and the intensity of
the highest unannotated peak. The product ions of peptides, glycans,
and glycopeptides in spectra are labeled in different class-type colors
to facilitate interpretation. MS_Piano assists validating peptide
and N-glycopeptide identification from database and library searches
and provides quality control and optimizes search reliability in custom
developed peptide mass spectral libraries. The software is freely
available in .exe and .dll formats for the Windows operating system.