Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization

Proteomics data-dependent acquisition data sets collected
with
high-resolution mass-spectrometry (MS) can achieve very high-quality
results, but nearly every analysis yields results that are thresholded
at some accepted false discovery rate, meaning that a substantial
number of results are incorrect. For study conclusions that rely on
a small number of peptide-spectrum matches being correct, it is thus
important to examine at least some crucial spectra to ensure that
they are not one of the incorrect identifications. We present Quetzal,
a peptide fragment ion spectrum annotation tool to assist researchers
in annotating and examining such spectra to ensure that they correctly
support study conclusions. We describe how Quetzal annotates spectra
using the new Human Proteome Organization (HUPO) Proteomics Standards
Initiative (PSI) mzPAF standard for fragment ion peak annotation,
including the Python-based code, a web-service end point that provides
annotation services, and a web-based application for annotating spectra
and producing publication-quality figures. We illustrate its functionality
with several annotated spectra of varying complexity. Quetzal provides
easily accessible functionality that can assist in the effort to ensure
and demonstrate that crucial spectra support study conclusions. Quetzal
is publicly available at https://proteomecentral.proteomexchange.org/quetzal/.