title: Benchmark study of automatic annotation of MALDI-TOF N-glycan profiles.
abstract: Human experts can annotate peaks in MALDI-TOF profiles of detached N-glycans with some degree of accuracy. Even though MALDI-TOF profiles give only intact masses without any fragmentation information, expert knowledge of the most common glycans and biosynthetic pathways in the biological system can point to a small set of most likely glycan structures at the "cartoon" level of detail. Cartoonist is a recently developed, fully automatic annotation tool for MALDI-TOF glycan profiles. Here we benchmark Cartoonist's automatic annotations against human expert annotations on human and mouse N-glycan data from the Consortium for Functional Glycomics. We find that Cartoonist and expert annotations largely agree, but the expert tends to annotate more specifically, meaning fewer suggested structures per peak, and Cartoonist more comprehensively, meaning more annotated peaks. On peaks for which both Cartoonist and the expert give unique cartoons, the two cartoons agree in over 90% of all cases. This article is part of a Special Issue entitled: Computational Proteomics.
authors.affiliation: Palo Alto Research Center, USA.
authors.forename: Alejandro E
authors.initials: AE
authors.lastname: Brito
authors.affiliation: Protein Metrics Inc., USA.
authors.forename: Doron
authors.initials: D
authors.lastname: Kletter
authors.affiliation: Palo Alto Research Center, USA.
authors.forename: Mudita
authors.initials: M
authors.lastname: Singhal
authors.affiliation: Protein Metrics Inc., USA. Electronic address: bern@proteinmetrics.com.
authors.forename: Marshall
authors.initials: M
authors.lastname: Bern
mesh_terms: D000465:Algorithms; D019985:Benchmarking; D002240:Carbohydrate Sequence; D006801:Humans; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011134:Polysaccharides / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D011134:Polysaccharides
keywords: Bioinformatics; Glycomics; Glycosylation; Mass spectrometry