MassyTools: A High-Throughput Targeted Data Processing Tool for Relative Quantitation and Quality Control Developed for Glycomic and Glycoproteomic MALDI-MS

The
study of N-linked glycosylation has long been complicated by
a lack of bioinformatics tools. In particular, there is still a lack
of fast and robust data processing tools for targeted (relative) quantitation.
We have developed modular, high-throughput data processing software,
MassyTools, that is capable of calibrating spectra, extracting data,
and performing quality control calculations based on a user-defined
list of glycan or glycopeptide compositions. Typical examples of output
include relative areas after background subtraction, isotopic pattern-based
quality scores, spectral quality scores, and signal-to-noise ratios.
We demonstrated MassyTools’ performance on MALDI-TOF-MS glycan
and glycopeptide data from different samples. MassyTools yielded better
calibration than the commercial software flexAnalysis, generally showing
2-fold better ppm errors after internal calibration. Relative quantitation
using MassyTools and flexAnalysis gave similar results, yielding a
relative standard deviation (RSD) of the main glycan of ∼6%.
However, MassyTools yielded 2- to 5-fold lower RSD values for low-abundant
analytes than flexAnalysis. Additionally, feature curation based on
the computed quality criteria improved the data quality. In conclusion,
we show that MassyTools is a robust automated data processing tool
for high-throughput, high-performance glycosylation analysis. The
package is released under the Apache 2.0 license and is freely available
on GitHub (https://github.com/Tarskin/MassyTools).