title: MassyTools: A High-Throughput Targeted Data Processing Tool for Relative Quantitation and Quality Control Developed for Glycomic and Glycoproteomic MALDI-MS.
abstract: 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 ).
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.
authors.forename: Bas C
authors.initials: BC
authors.lastname: Jansen
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.
authors.forename: Karli R
authors.initials: KR
authors.lastname: Reiding
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.|Department of Rheumatology, Erasmus University Medical Center , 3000 CA Rotterdam, The Netherlands.
authors.forename: Albert
authors.initials: A
authors.lastname: Bondt
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.
authors.forename: Agnes L
authors.initials: AL
authors.lastname: Hipgrave Ederveen
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.
authors.forename: Magnus
authors.initials: M
authors.lastname: Palmblad
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.
authors.forename: David
authors.initials: D
authors.lastname: Falck
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.|Division of BioAnalytical Chemistry, VU University Amsterdam , 1081 HV Amsterdam, The Netherlands.
authors.forename: Manfred
authors.initials: M
authors.lastname: Wuhrer
mesh_terms: D000911:Antibodies, Monoclonal / Q000032:analysis; D002138:Calibration; D001330:Electronic Data Processing / Q000379:methods; D054794:Glycomics / Q000379:methods*; D006020:Glycopeptides / Q000032:analysis; D006031:Glycosylation; D006801:Humans; D011134:Polysaccharides / Q000032:analysis; D011786:Quality Control; D059629:Signal-To-Noise Ratio; D012984:Software; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D000911:Antibodies, Monoclonal; D006020:Glycopeptides; D011134:Polysaccharides
keywords: Bioinformatics; biopharmaceuticals; glycomics; glycoproteomics; mass spectrometry; matrix-assisted laser desorption/ionization; profiling; quality control; relative quantitation