Automatic annotation of matrix‐assisted laser desorption/ionization N‐glycan spectra

Abstract

Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is the pre-eminent technique for mass mapping of glycans. In order to make this technique practical for high-throughput screening, reliable automatic methods of annotating peaks must be devised. We describe an algorithm called Cartoonist that labels peaks in MALDI spectra of permethylated N-glycans with cartoons which represent the most plausible glycans consistent with the peak masses and the types of glycans being analyzed. There are three main parts to Cartoonist. (i) It selects annotations from a library of biosynthetically plausible cartoons. The library we currently use has about 2800 cartoons, but was constructed using only about 300 archetype cartoons entered by hand. (ii) It determines the precision and calibration of the machine used to generate the spectrum. It does this automatically based on the spectrum itself. (iii) It assigns a confidence score to each annotation. In particular, rather than making a binary yes/no decision when annotating a peak, it makes all plausible annotations and associates them with scores indicating the probability that they are correct.

Activation of Murine CD4+ and CD8+ T Lymphocytes Leads to Dramatic Remodeling ofN-Linked Glycans

“…In contrast, the predominant dihexose-terminated biantennary glycan at mass 2653 in activated CD8 and CD4 cells is a minor peak in the profiles from fresh cells. More detailed annotations of the MS spectra, using the cartoonist algorithm (35), are provided in Fig. S1 (supplemental data).…”

A ratiometric lectin microarray approach to analysis of the dynamic mammalian glycome

“…Although great strides have been made in the use of this technique, mass spectrometry has difficulty in discriminating between the many structural isomers presented by glycans. In addition, mass spectrometry requires expensive equipment and time-consuming separation and annotation techniques (4,10). A typical glycomic analysis by mass spectrometry focuses on only a portion of the glycans (usually the N-linked fraction), and some critical substructures, such as sialic acids and sulfation of sugars, are often removed before analysis.…”

Glycoproteomics: Past, present and future

“…Calibration results together with isotope envelope shapes are then used to assign confidence scores to peak annotations. Finally, a graphical output is created by superimposition of the assigned structures on the actual spectra [37]. The Cartoonist algorithms continue to be developed with the objective of reducing the amount of prior expertise required [38].…”